modified: Makefile

	modified:   bin/wish/ctfDisplay/ctfDisplay.wish
	recompiled for X86MAC64:   hostdepend/X86MAC64/bin/X86MAC64/*
	recompiled for X86MAC64:   hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageSummationCalculate.sharedo

diff --git a/bin/X86MAC64/CheckCommonLineData b/bin/X86MAC64/CheckCommonLineData
index 9977372..3abbb7c 100755 (executable)
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diff --git a/bin/X86MAC64/CheckOfOrientation b/bin/X86MAC64/CheckOfOrientation
index 7065764..274c27c 100755 (executable)
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diff --git a/bin/X86MAC64/CheckOrientationByDegree b/bin/X86MAC64/CheckOrientationByDegree
index 1d71050..e965c6b 100755 (executable)
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diff --git a/bin/X86MAC64/CommonLineCalculation b/bin/X86MAC64/CommonLineCalculation
index 7c19107..442912d 100755 (executable)
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diff --git a/bin/X86MAC64/Descartes2Polar b/bin/X86MAC64/Descartes2Polar
index 49d8ce2..afff214 100755 (executable)
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diff --git a/bin/X86MAC64/Display2 b/bin/X86MAC64/Display2
index d8d4101..76e0fd2 100755 (executable)
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diff --git a/bin/X86MAC64/EvaluateCorrelationMapwithCommonLine b/bin/X86MAC64/EvaluateCorrelationMapwithCommonLine
index 70b3159..9c8eddf 100755 (executable)
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diff --git a/bin/X86MAC64/FETOrientationSearchByAnnealing b/bin/X86MAC64/FETOrientationSearchByAnnealing
index 3f0d9bf..34e6f5b 100755 (executable)
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diff --git a/bin/X86MAC64/FETOrientationSearchByFeatureAlignment b/bin/X86MAC64/FETOrientationSearchByFeatureAlignment
index ec433a1..04c862d 100755 (executable)
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diff --git a/bin/X86MAC64/FETmapOrientationSearchBySimultaneousFitting b/bin/X86MAC64/FETmapOrientationSearchBySimultaneousFitting
index 9817738..53b7b2f 100755 (executable)
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diff --git a/bin/X86MAC64/FETsmallMapSetCreate_forSimultaneousMinimization b/bin/X86MAC64/FETsmallMapSetCreate_forSimultaneousMinimization
index cd54b7e..e46acee 100755 (executable)
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diff --git a/bin/X86MAC64/LCalculationForOrientationSearch b/bin/X86MAC64/LCalculationForOrientationSearch
index e9c4714..f8fa605 100755 (executable)
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diff --git a/bin/X86MAC64/Polar2Descartes b/bin/X86MAC64/Polar2Descartes
index cce37dc..5ed2f1e 100755 (executable)
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diff --git a/bin/X86MAC64/ProjectionDirectionMapCreate b/bin/X86MAC64/ProjectionDirectionMapCreate
index fada0ec..0f21935 100755 (executable)
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diff --git a/bin/X86MAC64/WeightCalculationOfCommonLineSearch b/bin/X86MAC64/WeightCalculationOfCommonLineSearch
index f5fc9f9..0e40754 100755 (executable)
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diff --git a/bin/X86MAC64/WeightCalculationOfCommonLineSearchByAllSinogram b/bin/X86MAC64/WeightCalculationOfCommonLineSearchByAllSinogram
index 9e6e6c5..1bd0971 100755 (executable)
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diff --git a/bin/X86MAC64/array2mrc b/bin/X86MAC64/array2mrc
index 3d8c834..f48a2e3 100755 (executable)
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diff --git a/bin/X86MAC64/bin2mrc b/bin/X86MAC64/bin2mrc
index 2e778d1..8db3c33 100755 (executable)
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diff --git a/bin/X86MAC64/coordRotation b/bin/X86MAC64/coordRotation
index 3ad2185..41f0664 100755 (executable)
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diff --git a/bin/X86MAC64/ctfDeterminationFromMultiImage b/bin/X86MAC64/ctfDeterminationFromMultiImage
index b93d710..906fb1e 100755 (executable)
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diff --git a/bin/X86MAC64/ctfDeterminationFromThonRing b/bin/X86MAC64/ctfDeterminationFromThonRing
index 34524ad..ddeb30c 100755 (executable)
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diff --git a/bin/X86MAC64/ctfDetermine b/bin/X86MAC64/ctfDetermine
index 2bfdcb5..93b6cd3 100755 (executable)
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diff --git a/bin/X86MAC64/ctfDisplay b/bin/X86MAC64/ctfDisplay
index 23fc924..33ea331 100755 (executable)
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diff --git a/bin/X86MAC64/ctfEnvelopFunction b/bin/X86MAC64/ctfEnvelopFunction
index cd27313..2f56490 100755 (executable)
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diff --git a/bin/X86MAC64/ctfFunction b/bin/X86MAC64/ctfFunction
index 14a7aaa..1821779 100755 (executable)
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diff --git a/bin/X86MAC64/ctfInfoSet b/bin/X86MAC64/ctfInfoSet
index 8558b3a..90861a0 100755 (executable)
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diff --git a/bin/X86MAC64/ctfMultiFunction b/bin/X86MAC64/ctfMultiFunction
index ccb008b..93024cc 100755 (executable)
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diff --git a/bin/X86MAC64/ctfWeightMapCreation b/bin/X86MAC64/ctfWeightMapCreation
index 8778aa3..104e06c 100755 (executable)
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diff --git a/bin/X86MAC64/defocusDeterminationFromThonRing b/bin/X86MAC64/defocusDeterminationFromThonRing
index d8a5fa3..3ce13bb 100755 (executable)
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diff --git a/bin/X86MAC64/dos2unix b/bin/X86MAC64/dos2unix
index 4da5ce8..fc75fe9 100755 (executable)
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diff --git a/bin/X86MAC64/electronWaveLength b/bin/X86MAC64/electronWaveLength
index 7e63cc6..f62d8ed 100755 (executable)
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diff --git a/bin/X86MAC64/emData2mrc b/bin/X86MAC64/emData2mrc
index 6c5fbaf..9a860c8 100755 (executable)
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diff --git a/bin/X86MAC64/energyTransferModelResultCheck b/bin/X86MAC64/energyTransferModelResultCheck
index 2844342..07e07ed 100755 (executable)
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diff --git a/bin/X86MAC64/gmolvie b/bin/X86MAC64/gmolvie
index a4ac408..44e07a0 100755 (executable)
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diff --git a/bin/X86MAC64/imagesView b/bin/X86MAC64/imagesView
index 308c175..a0f7ef9 100755 (executable)
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diff --git a/bin/X86MAC64/imodst2mrc b/bin/X86MAC64/imodst2mrc
index 8788388..af3da13 100755 (executable)
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diff --git a/bin/X86MAC64/ip2mrc b/bin/X86MAC64/ip2mrc
index fc7a111..baf894c 100755 (executable)
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diff --git a/bin/X86MAC64/largeIPInfo b/bin/X86MAC64/largeIPInfo
index a04f26c..9f596f4 100755 (executable)
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diff --git a/bin/X86MAC64/ll2ltlg b/bin/X86MAC64/ll2ltlg
index 547445e..d8a2f62 100755 (executable)
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diff --git a/bin/X86MAC64/llDataAverage b/bin/X86MAC64/llDataAverage
index cdabaeb..b77cba7 100755 (executable)
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diff --git a/bin/X86MAC64/llDataAxisSearch b/bin/X86MAC64/llDataAxisSearch
index b5f0587..594ff67 100755 (executable)
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diff --git a/bin/X86MAC64/llDataCTFCompensate b/bin/X86MAC64/llDataCTFCompensate
index cf4fc07..7c282ac 100755 (executable)
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diff --git a/bin/X86MAC64/llDataCompare b/bin/X86MAC64/llDataCompare
index d13128e..ccc758d 100755 (executable)
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diff --git a/bin/X86MAC64/llDataContributionCalcDifferentN b/bin/X86MAC64/llDataContributionCalcDifferentN
index d495202..66ca5b5 100755 (executable)
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diff --git a/bin/X86MAC64/llDataDump b/bin/X86MAC64/llDataDump
index a41f3e5..57058f0 100755 (executable)
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diff --git a/bin/X86MAC64/llDataEquatorAdd b/bin/X86MAC64/llDataEquatorAdd
index 17ffb3c..d68404e 100755 (executable)
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diff --git a/bin/X86MAC64/llDataExtract b/bin/X86MAC64/llDataExtract
index d70587c..6f24268 100755 (executable)
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diff --git a/bin/X86MAC64/llDataFit b/bin/X86MAC64/llDataFit
index d433956..3921e2a 100755 (executable)
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diff --git a/bin/X86MAC64/llDataInfo b/bin/X86MAC64/llDataInfo
index 9ce3fd1..6c42894 100755 (executable)
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diff --git a/bin/X86MAC64/llDataLowPassFiltering b/bin/X86MAC64/llDataLowPassFiltering
index 723f78f..f033e32 100755 (executable)
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diff --git a/bin/X86MAC64/llDataMultiCTFCompensation b/bin/X86MAC64/llDataMultiCTFCompensation
index 2b187a3..ac58973 100755 (executable)
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diff --git a/bin/X86MAC64/llDataNEstimation b/bin/X86MAC64/llDataNEstimation
index 71973ce..39d125f 100755 (executable)
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diff --git a/bin/X86MAC64/llDataNormalization b/bin/X86MAC64/llDataNormalization
index 7a41daf..c2c1741 100755 (executable)
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diff --git a/bin/X86MAC64/llDataPrint b/bin/X86MAC64/llDataPrint
index 7eeb73b..c7fc282 100755 (executable)
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diff --git a/bin/X86MAC64/llDataRescaling b/bin/X86MAC64/llDataRescaling
index 93062ae..5110379 100755 (executable)
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diff --git a/bin/X86MAC64/llDataResolutionCheck b/bin/X86MAC64/llDataResolutionCheck
index 91b040a..2bbf381 100755 (executable)
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diff --git a/bin/X86MAC64/llDataSelectionEstimation b/bin/X86MAC64/llDataSelectionEstimation
index cffe0cc..f1cc07e 100755 (executable)
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diff --git a/bin/X86MAC64/llDataWeightSet b/bin/X86MAC64/llDataWeightSet
index 0b7f76e..53a811f 100755 (executable)
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diff --git a/bin/X86MAC64/llDatarMaxLimit b/bin/X86MAC64/llDatarMaxLimit
index 6c7f46d..abd8b00 100755 (executable)
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diff --git a/bin/X86MAC64/llExtract b/bin/X86MAC64/llExtract
index ba043d0..87ba701 100755 (executable)
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diff --git a/bin/X86MAC64/llExtractCtfinfFileCreate b/bin/X86MAC64/llExtractCtfinfFileCreate
index d6bde20..86826fb 100755 (executable)
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diff --git a/bin/X86MAC64/llExtractCtrlFileCreate b/bin/X86MAC64/llExtractCtrlFileCreate
index 463469f..c91e8be 100755 (executable)
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diff --git a/bin/X86MAC64/llExtractWithLayerSeparation b/bin/X86MAC64/llExtractWithLayerSeparation
index f071f0b..412261d 100755 (executable)
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diff --git a/bin/X86MAC64/llExtractWithLayerSeparationCtrlFileCreate b/bin/X86MAC64/llExtractWithLayerSeparationCtrlFileCreate
index 91e7a4e..0c8b618 100755 (executable)
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diff --git a/bin/X86MAC64/llExtractWithLayerSeparationCtrlFileCreateMyosin b/bin/X86MAC64/llExtractWithLayerSeparationCtrlFileCreateMyosin
index f4501ef..43436c4 100755 (executable)
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diff --git a/bin/X86MAC64/llExtractWithLayerSeparationFilamentInfo b/bin/X86MAC64/llExtractWithLayerSeparationFilamentInfo
index 46dbc1c..70ea98c 100755 (executable)
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diff --git a/bin/X86MAC64/ltlg2mrc b/bin/X86MAC64/ltlg2mrc
index 11360a9..268984a 100755 (executable)
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diff --git a/bin/X86MAC64/ltlgDataInfo b/bin/X86MAC64/ltlgDataInfo
index 427ab55..d0274f1 100755 (executable)
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diff --git a/bin/X86MAC64/matrix3DEulerAngleTransform b/bin/X86MAC64/matrix3DEulerAngleTransform
index ab66916..5cb57d1 100755 (executable)
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diff --git a/bin/X86MAC64/matrix3DFromEulerAngle b/bin/X86MAC64/matrix3DFromEulerAngle
index 5930a04..6d150ad 100755 (executable)
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diff --git a/bin/X86MAC64/matrix3DInverse b/bin/X86MAC64/matrix3DInverse
index 8e39040..33cc542 100755 (executable)
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diff --git a/bin/X86MAC64/matrix3DToEulerAngle b/bin/X86MAC64/matrix3DToEulerAngle
index 57e2bb8..6c81e7a 100755 (executable)
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diff --git a/bin/X86MAC64/moi2mrc b/bin/X86MAC64/moi2mrc
index 0b48ee9..db7952c 100755 (executable)
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diff --git a/bin/X86MAC64/molecularEnvelopeResampling b/bin/X86MAC64/molecularEnvelopeResampling
index f501c61..5009f2d 100755 (executable)
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diff --git a/bin/X86MAC64/mrc2Dto3D b/bin/X86MAC64/mrc2Dto3D
index 2e3862d..f39e7e2 100755 (executable)
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diff --git a/bin/X86MAC64/mrc2fld b/bin/X86MAC64/mrc2fld
index 8206d1a..3f18cd8 100755 (executable)
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diff --git a/bin/X86MAC64/mrc2gif b/bin/X86MAC64/mrc2gif
index f8b46e1..132c029 100755 (executable)
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diff --git a/bin/X86MAC64/mrc2map b/bin/X86MAC64/mrc2map
index 5f41b5e..835acdf 100755 (executable)
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diff --git a/bin/X86MAC64/mrc2mrc b/bin/X86MAC64/mrc2mrc
new file mode 100755 (executable)
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diff --git a/bin/X86MAC64/mrc2tiff b/bin/X86MAC64/mrc2tiff
index acad3e3..86ac283 100755 (executable)
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diff --git a/bin/X86MAC64/mrc3DExtractZ b/bin/X86MAC64/mrc3DExtractZ
index 6e65a07..45de2ac 100755 (executable)
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diff --git a/bin/X86MAC64/mrc3Dto2D b/bin/X86MAC64/mrc3Dto2D
index 7b59dc0..f0b757f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFETnormalizeBySD b/bin/X86MAC64/mrcFETnormalizeBySD
index 57f26a2..5043a68 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTBandPassFilter b/bin/X86MAC64/mrcFFTBandPassFilter
index 5426a9e..09c3847 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTCTFCompensation b/bin/X86MAC64/mrcFFTCTFCompensation
index 6561501..dcffd9d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTDigitize b/bin/X86MAC64/mrcFFTDigitize
index 682bfd0..2466b55 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTExpression b/bin/X86MAC64/mrcFFTExpression
index 40366f1..05bafa9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTFibreDiagram b/bin/X86MAC64/mrcFFTFibreDiagram
index 16c529f..6206b2a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTFiltering b/bin/X86MAC64/mrcFFTFiltering
index d033e53..5756b32 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTIQEstimation b/bin/X86MAC64/mrcFFTIQEstimation
index 2aadad6..878e9a6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTInfo b/bin/X86MAC64/mrcFFTInfo
index e84bffe..4544844 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTLayerLineCheck b/bin/X86MAC64/mrcFFTLayerLineCheck
index c6b47af..4bbc408 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTMedianFilter b/bin/X86MAC64/mrcFFTMedianFilter
index 174ae9b..51e4db7 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTProjection b/bin/X86MAC64/mrcFFTProjection
index 823f2b0..1364f53 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTResampling b/bin/X86MAC64/mrcFFTResampling
index 4f5bb30..69ddda0 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTShellInfo b/bin/X86MAC64/mrcFFTShellInfo
index d17a7f4..e992cea 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTSizeChange b/bin/X86MAC64/mrcFFTSizeChange
index 2297de1..7fd9bad 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTSpectrum b/bin/X86MAC64/mrcFFTSpectrum
index 4f6c4aa..0189f99 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTXFiltering b/bin/X86MAC64/mrcFFTXFiltering
index add48e4..3edf450 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFFTplainreduce b/bin/X86MAC64/mrcFFTplainreduce
index 6e79a81..05e6581 100755 (executable)
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diff --git a/bin/X86MAC64/mrcFTMeridianEquatorRedece b/bin/X86MAC64/mrcFTMeridianEquatorRedece
index baba46d..a2cc55e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage1DProjectionfrom2D b/bin/X86MAC64/mrcImage1DProjectionfrom2D
index 7f83b1f..86dd092 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage1dAverageByCorrelation b/bin/X86MAC64/mrcImage1dAverageByCorrelation
index 7cc6be4..5af4a8f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage1dShiftAverageByAnnealing b/bin/X86MAC64/mrcImage1dShiftAverageByAnnealing
index aa02f0c..6862fcc 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage1dShiftByCorrelation b/bin/X86MAC64/mrcImage1dShiftByCorrelation
index e9af4af..63acefa 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage2DBackProjection b/bin/X86MAC64/mrcImage2DBackProjection
index 238fd01..c461ad0 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage2DProjection b/bin/X86MAC64/mrcImage2DProjection
index 85b00c3..a66cf1c 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage2pdb b/bin/X86MAC64/mrcImage2pdb
index 76ef416..60e016f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage3DHighResoEmphasis b/bin/X86MAC64/mrcImage3DHighResoEmphasis
index c379a15..d5a174e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage3DPad b/bin/X86MAC64/mrcImage3DPad
index bde2723..d66e7eb 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage3DPad2 b/bin/X86MAC64/mrcImage3DPad2
index 5ef357b..7a1f729 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImage3DSymmetryFind b/bin/X86MAC64/mrcImage3DSymmetryFind
new file mode 100755 (executable)
index 0000000..a37390c
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diff --git a/bin/X86MAC64/mrcImage3DWindowing b/bin/X86MAC64/mrcImage3DWindowing
index b159c34..b106fc2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAbnormalValueRemove b/bin/X86MAC64/mrcImageAbnormalValueRemove
index bd6dcd0..4c4ccd9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageActinSingleParticleAnalysis b/bin/X86MAC64/mrcImageActinSingleParticleAnalysis
index 1428620..a133bbf 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAdaptiveBinalization b/bin/X86MAC64/mrcImageAdaptiveBinalization
index eef3308..abba9b6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAdd b/bin/X86MAC64/mrcImageAdd
index c674901..4fee6bd 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAddValue b/bin/X86MAC64/mrcImageAddValue
index 69d4970..6c3f333 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAreaCalc b/bin/X86MAC64/mrcImageAreaCalc
index c2ee8e5..e3d7339 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAssignedToTFofPDB b/bin/X86MAC64/mrcImageAssignedToTFofPDB
index 40c0167..59d91e6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAutoCorrelationWithWindowing b/bin/X86MAC64/mrcImageAutoCorrelationWithWindowing
index 02a63b1..10cb5d0 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAutoFilamentExtract b/bin/X86MAC64/mrcImageAutoFilamentExtract
index b94f5b7..de07b2f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAutoFilamentExtractResultAnalysis b/bin/X86MAC64/mrcImageAutoFilamentExtractResultAnalysis
index 09c05d1..1e0b176 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAutoRotationCorrelation b/bin/X86MAC64/mrcImageAutoRotationCorrelation
index 26b1b36..7b2203c 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAutoRotationCorrelation3D b/bin/X86MAC64/mrcImageAutoRotationCorrelation3D
index b6c347b..cca0497 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageAverage b/bin/X86MAC64/mrcImageAverage
index ef68cf4..fd2c6ee 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageBandPassFilter b/bin/X86MAC64/mrcImageBandPassFilter
index a424941..463a926 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageBilateralFilter b/bin/X86MAC64/mrcImageBilateralFilter
index b952a19..b0beebc 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageBinalization b/bin/X86MAC64/mrcImageBinalization
index 9467881..0c844ad 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageBlockMerge b/bin/X86MAC64/mrcImageBlockMerge
index e358fc9..0fca7c2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageBoundaryInfo b/bin/X86MAC64/mrcImageBoundaryInfo
index 1428620..a133bbf 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCCDNoiseRemove b/bin/X86MAC64/mrcImageCCDNoiseRemove
index f013efe..865410d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCTFCompensation b/bin/X86MAC64/mrcImageCTFCompensation
index f685a08..73066e5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCTFCompensationForTiltImage b/bin/X86MAC64/mrcImageCTFCompensationForTiltImage
index aabb20c..91492e9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCTFDetermination b/bin/X86MAC64/mrcImageCTFDetermination
index 187f3c1..cfeb480 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCTFObservation b/bin/X86MAC64/mrcImageCTFObservation
index af36cdf..8f26a67 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCTFSN b/bin/X86MAC64/mrcImageCTFSN
index 93caaf2..6e7568d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCVE b/bin/X86MAC64/mrcImageCVE
index afc5079..1b8caf2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCenterDensityChange b/bin/X86MAC64/mrcImageCenterDensityChange
index 02527a9..c8d1b19 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCenterGet b/bin/X86MAC64/mrcImageCenterGet
index dc04753..4fe8215 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCenterOfMassCalculate b/bin/X86MAC64/mrcImageCenterOfMassCalculate
index c202013..c7c1f5c 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCircumferentialProjection b/bin/X86MAC64/mrcImageCircumferentialProjection
index 8e7a439..b4eb793 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageClosing b/bin/X86MAC64/mrcImageClosing
index 1acc137..59ef741 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageColoring b/bin/X86MAC64/mrcImageColoring
index 825ee37..2c0d4e9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCommonLineSearch b/bin/X86MAC64/mrcImageCommonLineSearch
index 1747d91..da98733 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageConnection b/bin/X86MAC64/mrcImageConnection
index 98e3d02..e2e4120 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageConnectivityNumberCalc b/bin/X86MAC64/mrcImageConnectivityNumberCalc
index 800ee31..b3878df 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageContourSurfaceCreate b/bin/X86MAC64/mrcImageContourSurfaceCreate
index d87bd70..2924d67 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageConvolution b/bin/X86MAC64/mrcImageConvolution
index 3967575..9e90754 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCoordinateChange b/bin/X86MAC64/mrcImageCoordinateChange
index ab41a70..02b337c 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCoreImageCalc b/bin/X86MAC64/mrcImageCoreImageCalc
index 768d857..7466732 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCorrelation b/bin/X86MAC64/mrcImageCorrelation
index 84127e4..815aadb 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCorrelationInFourierSpace b/bin/X86MAC64/mrcImageCorrelationInFourierSpace
index b227118..4b2ab5b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCrystalCreate b/bin/X86MAC64/mrcImageCrystalCreate
index 80c4aa1..4a2fe33 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageCylinderSection b/bin/X86MAC64/mrcImageCylinderSection
index bd4d320..2c955a5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDeadPixelCorrection b/bin/X86MAC64/mrcImageDeadPixelCorrection
index 0193d22..5c76954 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDensityChangeEstimation b/bin/X86MAC64/mrcImageDensityChangeEstimation
index 98f9c90..d2726b2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDensityInfo b/bin/X86MAC64/mrcImageDensityInfo
index 1481900..4fb12a1 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDensityNormalization b/bin/X86MAC64/mrcImageDensityNormalization
index ed44b8e..31ada27 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDensityNormalizationByImage b/bin/X86MAC64/mrcImageDensityNormalizationByImage
index 57a2971..b804d9b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDilation b/bin/X86MAC64/mrcImageDilation
index b898242..d33d596 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDisplayDensityAsTempFactor b/bin/X86MAC64/mrcImageDisplayDensityAsTempFactor
index 25a8c9b..b74fcea 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDistanceConversion b/bin/X86MAC64/mrcImageDistanceConversion
index 33d66e9..7d0480c 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDivideInfoForTomography b/bin/X86MAC64/mrcImageDivideInfoForTomography
index ba18c8c..52e9b74 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageDivideIntoTwoImages b/bin/X86MAC64/mrcImageDivideIntoTwoImages
index 6f5dd16..03d25b6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageEdgeImageGet b/bin/X86MAC64/mrcImageEdgeImageGet
index 9bae648..556c310 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageErosion b/bin/X86MAC64/mrcImageErosion
index 50d9c54..9c73ab7 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageEstimateTiltImage b/bin/X86MAC64/mrcImageEstimateTiltImage
index 2994254..075a5bc 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageExpression b/bin/X86MAC64/mrcImageExpression
index 1cbf798..ec8e813 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFFT b/bin/X86MAC64/mrcImageFFT
index d8dde68..87de9f4 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFFTLayerLineExtraction b/bin/X86MAC64/mrcImageFFTLayerLineExtraction
index e5f6bb7..130c723 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFOMCalc b/bin/X86MAC64/mrcImageFOMCalc
index 8e05814..a3982c9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFeatureExtraction b/bin/X86MAC64/mrcImageFeatureExtraction
index 1884377..f3b6bfc 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFilterCreate b/bin/X86MAC64/mrcImageFilterCreate
index 7fd5b05..372f1a7 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFilteringbyFile b/bin/X86MAC64/mrcImageFilteringbyFile
index c0efe7e..930b666 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFilteringbyFileForVariance b/bin/X86MAC64/mrcImageFilteringbyFileForVariance
index 0997eec..60308eb 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFourierShellCorrelation b/bin/X86MAC64/mrcImageFourierShellCorrelation
index 9867021..354fa11 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageFractalFourierShellCorrelation b/bin/X86MAC64/mrcImageFractalFourierShellCorrelation
index 0b675b0..6979558 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageGaussDisc b/bin/X86MAC64/mrcImageGaussDisc
index 60b1bf4..d8f6b6a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageGaussSphere b/bin/X86MAC64/mrcImageGaussSphere
index fec993e..c89b109 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHeaderChange b/bin/X86MAC64/mrcImageHeaderChange
index fac6e1b..a87400c 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHelicalAveraging b/bin/X86MAC64/mrcImageHelicalAveraging
index 5769278..421797d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHelicalMappingFrom2DImage b/bin/X86MAC64/mrcImageHelicalMappingFrom2DImage
index b90cb3d..f82410e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHelicalMasking b/bin/X86MAC64/mrcImageHelicalMasking
index 3d16030..5380697 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHelicalMaskingBy2DImage b/bin/X86MAC64/mrcImageHelicalMaskingBy2DImage
index 18833f0..6e0eb2e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHelicalProjection b/bin/X86MAC64/mrcImageHelicalProjection
index 4100209..0f7479a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHighPassFilter b/bin/X86MAC64/mrcImageHighPassFilter
index 66ab2d5..663706f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageHighlighting b/bin/X86MAC64/mrcImageHighlighting
new file mode 100755 (executable)
index 0000000..ee66543
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diff --git a/bin/X86MAC64/mrcImageInfo b/bin/X86MAC64/mrcImageInfo
index ed32f2a..7f7d0b0 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageInverseRadonTransform b/bin/X86MAC64/mrcImageInverseRadonTransform
index 302bde7..e7b27f6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageLabeling b/bin/X86MAC64/mrcImageLabeling
index f233999..40a9ded 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageLowPassFilter b/bin/X86MAC64/mrcImageLowPassFilter
index f1f77ce..a028355 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMagnificationChange b/bin/X86MAC64/mrcImageMagnificationChange
index f8027fa..0b1833d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMake2DArrayImage b/bin/X86MAC64/mrcImageMake2DArrayImage
index 5d36435..355dd61 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMakeCylinder b/bin/X86MAC64/mrcImageMakeCylinder
index 48ac32f..6d40769 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMakeDump b/bin/X86MAC64/mrcImageMakeDump
index 95ab74e..93847e1 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMakeFromTextFile b/bin/X86MAC64/mrcImageMakeFromTextFile
index bafe3e7..50343df 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMakeSphere b/bin/X86MAC64/mrcImageMakeSphere
index c8bdaa4..2d0bcee 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMappingtoPdb b/bin/X86MAC64/mrcImageMappingtoPdb
index bf7d422..708af7d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMasking b/bin/X86MAC64/mrcImageMasking
index 8736bfe..e6d8421 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMaskingByImage b/bin/X86MAC64/mrcImageMaskingByImage
index bedd9f1..26eada2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMergebyside b/bin/X86MAC64/mrcImageMergebyside
index 6c22ba6..02a5cd2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMirroring b/bin/X86MAC64/mrcImageMirroring
index 174b431..a625805 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageModeChange b/bin/X86MAC64/mrcImageModeChange
index b8d512b..bf98ff3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageModelCreate b/bin/X86MAC64/mrcImageModelCreate
index 1a01d8a..b47a94b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageModelSubfilamentsCreate b/bin/X86MAC64/mrcImageModelSubfilamentsCreate
index 091785e..74e9013 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMontageCreate b/bin/X86MAC64/mrcImageMontageCreate
index 5d8ed53..66369db 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMove b/bin/X86MAC64/mrcImageMove
index be9d499..73ad73b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMultiCTFCompensation b/bin/X86MAC64/mrcImageMultiCTFCompensation
index b08cdda..8bdb0a7 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMultiCTFDetermination b/bin/X86MAC64/mrcImageMultiCTFDetermination
index 469837f..4f8d9ce 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMultiplying b/bin/X86MAC64/mrcImageMultiplying
index c0a6fb2..3d3d1ea 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageMultiplyingbyFile b/bin/X86MAC64/mrcImageMultiplyingbyFile
index 4c5f883..b68b8d7 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNLMeansFilter b/bin/X86MAC64/mrcImageNLMeansFilter
index 3f53d4c..b50e6dc 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNeuralNetParticleLearning b/bin/X86MAC64/mrcImageNeuralNetParticleLearning
index 3e3b499..a366515 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNfoldAxisSearch b/bin/X86MAC64/mrcImageNfoldAxisSearch
index cf1ff5d..05a2325 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNoiseAdd b/bin/X86MAC64/mrcImageNoiseAdd
index 1930655..f8a65d4 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNoiseCreate b/bin/X86MAC64/mrcImageNoiseCreate
index 900fc96..8af96c9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNoiseReductionByRelaxation b/bin/X86MAC64/mrcImageNoiseReductionByRelaxation
index 635f92e..bbfe999 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNormalizedSubtraction b/bin/X86MAC64/mrcImageNormalizedSubtraction
index 89b1f82..16615e2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNormalizing b/bin/X86MAC64/mrcImageNormalizing
index f8c4118..08ec23e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageNullImageCreate b/bin/X86MAC64/mrcImageNullImageCreate
index aa3c590..eff3836 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageOddBoxel b/bin/X86MAC64/mrcImageOddBoxel
index 3f30575..a6e4a85 100755 (executable)
Binary files a/bin/X86MAC64/mrcImageOddBoxel and b/bin/X86MAC64/mrcImageOddBoxel differ

diff --git a/bin/X86MAC64/mrcImageOneLineSimilarityCalc b/bin/X86MAC64/mrcImageOneLineSimilarityCalc
index b2ce62e..814d3c5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageOpening b/bin/X86MAC64/mrcImageOpening
index 8610daf..66eed8a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageOrientationSearch b/bin/X86MAC64/mrcImageOrientationSearch
index 5c3ab5d..0f11b06 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageOrientationSearchByHigherSelection b/bin/X86MAC64/mrcImageOrientationSearchByHigherSelection
index f74689d..69e0cb2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageOrientationSearchByHybridization b/bin/X86MAC64/mrcImageOrientationSearchByHybridization
index f90a4e2..47cefb4 100755 (executable)
Binary files a/bin/X86MAC64/mrcImageOrientationSearchByHybridization and b/bin/X86MAC64/mrcImageOrientationSearchByHybridization differ

diff --git a/bin/X86MAC64/mrcImagePCA b/bin/X86MAC64/mrcImagePCA
index 9a5a5ee..6ad459e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePad b/bin/X86MAC64/mrcImagePad
index b1c4a78..83233c5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePanoramaCreate b/bin/X86MAC64/mrcImagePanoramaCreate
new file mode 100755 (executable)
index 0000000..6f2d067
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diff --git a/bin/X86MAC64/mrcImageParticleCandidateExtract b/bin/X86MAC64/mrcImageParticleCandidateExtract
index 4d8519e..3bf7e7d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePeakSearch b/bin/X86MAC64/mrcImagePeakSearch
index f57f30d..087aeec 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO b/bin/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO
index 1428620..a133bbf 100755 (executable)
Binary files a/bin/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO and b/bin/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO differ

diff --git a/bin/X86MAC64/mrcImagePixelDataGet b/bin/X86MAC64/mrcImagePixelDataGet
index 56e8df3..b3dc77a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePolyROI b/bin/X86MAC64/mrcImagePolyROI
index 5426a9e..09c3847 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePosterization b/bin/X86MAC64/mrcImagePosterization
index 0f1f6c1..33401e3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePrint b/bin/X86MAC64/mrcImagePrint
index 7489ff1..e64030f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagePrint3D b/bin/X86MAC64/mrcImagePrint3D
index 4383f44..cd771fc 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageProjection b/bin/X86MAC64/mrcImageProjection
index cf60adc..a78125b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageROI b/bin/X86MAC64/mrcImageROI
index e6e4c3b..c750e50 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageROI3D b/bin/X86MAC64/mrcImageROI3D
index de83a99..9330219 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageROIs b/bin/X86MAC64/mrcImageROIs
index b82ee3b..7cb7440 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageROItoPCAoutputImage b/bin/X86MAC64/mrcImageROItoPCAoutputImage
index 53140d4..37abe69 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRadialDistribution b/bin/X86MAC64/mrcImageRadialDistribution
index 4755cba..71b2ae4 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRadonTransform b/bin/X86MAC64/mrcImageRadonTransform
index d2e094e..b30da7a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRandomParticlesImageCreate b/bin/X86MAC64/mrcImageRandomParticlesImageCreate
index 53a836f..c3b652d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRealValueAdd b/bin/X86MAC64/mrcImageRealValueAdd
index 96c1864..6e4219b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRectangleGet b/bin/X86MAC64/mrcImageRectangleGet
index 91c8fc6..73cf380 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRectangleGetByCorrelation b/bin/X86MAC64/mrcImageRectangleGetByCorrelation
index 6ac9fd6..dce20f3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRefConv2D b/bin/X86MAC64/mrcImageRefConv2D
index 1045f0c..4f4c629 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRefCreate b/bin/X86MAC64/mrcImageRefCreate
index 73fc1db..9d656d0 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRefFFTConv2D b/bin/X86MAC64/mrcImageRefFFTConv2D
index fa98f5a..27c2107 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRefScaleChangeWithPad b/bin/X86MAC64/mrcImageRefScaleChangeWithPad
index 98c13e6..e31b9b9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageResolutionEstimateForFilaments b/bin/X86MAC64/mrcImageResolutionEstimateForFilaments
index 38649f3..527c5fa 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageReverse b/bin/X86MAC64/mrcImageReverse
index f67b720..6ee73a3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRotation b/bin/X86MAC64/mrcImageRotation
index faabd15..d0b420e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageRotation3D b/bin/X86MAC64/mrcImageRotation3D
index 3850450..8aa0ea8 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSN b/bin/X86MAC64/mrcImageSN
index 72fa2a2..9a19605 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSamplingUnitChange b/bin/X86MAC64/mrcImageSamplingUnitChange
index f399236..af9dd88 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageScalarAdd b/bin/X86MAC64/mrcImageScalarAdd
index 3cce663..9e4510e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSectionGet b/bin/X86MAC64/mrcImageSectionGet
index 0779c91..c35d9c3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSetFunction b/bin/X86MAC64/mrcImageSetFunction
index 5091aa4..5ece301 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageShapeOrientation b/bin/X86MAC64/mrcImageShapeOrientation
new file mode 100755 (executable)
index 0000000..1dec128
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diff --git a/bin/X86MAC64/mrcImageShapePCA b/bin/X86MAC64/mrcImageShapePCA
index 1d3d544..4467bb3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageShapePCAFit b/bin/X86MAC64/mrcImageShapePCAFit
index dcdee69..e57ab50 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageShift b/bin/X86MAC64/mrcImageShift
index 822cae9..a965af6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageShiftFollowingGC b/bin/X86MAC64/mrcImageShiftFollowingGC
index 392b9ec..9524e23 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageShrink b/bin/X86MAC64/mrcImageShrink
index 0e4d7b8..243fbf6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSiemensStar b/bin/X86MAC64/mrcImageSiemensStar
index 190dd7f..ee9ba69 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSimilarImageSearch b/bin/X86MAC64/mrcImageSimilarImageSearch
index 5426a9e..09c3847 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSimilarityEstimate b/bin/X86MAC64/mrcImageSimilarityEstimate
index 1238b51..cd45a67 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSinogramCorrelation b/bin/X86MAC64/mrcImageSinogramCorrelation
index 86e855a..5211598 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSinogramCreate b/bin/X86MAC64/mrcImageSinogramCreate
index 7956a86..5b89a3d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSinogramFFT b/bin/X86MAC64/mrcImageSinogramFFT
index ab6f20f..2a943a7 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSmoothing b/bin/X86MAC64/mrcImageSmoothing
index 16a5b74..714b217 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSolventFlattening b/bin/X86MAC64/mrcImageSolventFlattening
index 08340fd..2c8098a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSphere b/bin/X86MAC64/mrcImageSphere
index 8777cd2..3fd198a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSplit b/bin/X86MAC64/mrcImageSplit
index f66f042..463aa35 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSquare b/bin/X86MAC64/mrcImageSquare
index 789bea2..4050498 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageStandardDeviation b/bin/X86MAC64/mrcImageStandardDeviation
index 783ff46..2a5d286 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSubtraction b/bin/X86MAC64/mrcImageSubtraction
index ce0aa6a..92842db 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSuperResolution b/bin/X86MAC64/mrcImageSuperResolution
index 8fb9e20..78be74f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSymmetryAverage b/bin/X86MAC64/mrcImageSymmetryAverage
index c5829e2..0fec586 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSymmetryCentreFind b/bin/X86MAC64/mrcImageSymmetryCentreFind
index f4adb61..2d38772 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageSymmetryFind b/bin/X86MAC64/mrcImageSymmetryFind
index 0029004..b726de4 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageTfunction b/bin/X86MAC64/mrcImageTfunction
index 03843b2..4ccbd8c 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageTiltAxisSearch b/bin/X86MAC64/mrcImageTiltAxisSearch
index bb70fa5..b1491ed 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageTiltAxisSearchHelp b/bin/X86MAC64/mrcImageTiltAxisSearchHelp
index 6b5048e..3de30b9 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageToNAMDConstantForces b/bin/X86MAC64/mrcImageToNAMDConstantForces
index d7a050a..57672bb 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageToPointsSet b/bin/X86MAC64/mrcImageToPointsSet
index f821ce1..1490226 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageTrans b/bin/X86MAC64/mrcImageTrans
index 6ca4af1..5d7a2c3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageTransformDescartesIntoPolar b/bin/X86MAC64/mrcImageTransformDescartesIntoPolar
index f4cb52b..60c331a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageTransformSign b/bin/X86MAC64/mrcImageTransformSign
index 352f9dd..4470c51 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageTranspose b/bin/X86MAC64/mrcImageTranspose
index 694fa16..9c69f5d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageUnbentROI b/bin/X86MAC64/mrcImageUnbentROI
index 1b612b0..ea08a9e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageUnexpectedMassFromPDB b/bin/X86MAC64/mrcImageUnexpectedMassFromPDB
index b0303c0..7eda15e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageUntwist b/bin/X86MAC64/mrcImageUntwist
index 87a235d..29633e4 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageVarianceAnalysis b/bin/X86MAC64/mrcImageVarianceAnalysis
index bf45adf..e3ad3a6 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageVarianceMap b/bin/X86MAC64/mrcImageVarianceMap
index 4d53803..f7e1e70 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageVolumeCalc b/bin/X86MAC64/mrcImageVolumeCalc
index a9b8da2..24f8cb2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageWindowing b/bin/X86MAC64/mrcImageWindowing
index c046934..f3000c2 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImageZPad b/bin/X86MAC64/mrcImageZPad
index 9d36a2c..b4933c4 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagepdbFileReduce b/bin/X86MAC64/mrcImagepdbFileReduce
index ab27a2d..cfce809 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagesSinogramCorrelation b/bin/X86MAC64/mrcImagesSinogramCorrelation
index 52a9819..f5cc8ba 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImagestoRef b/bin/X86MAC64/mrcImagestoRef
index d783fce..c77408d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcImateToPointsSet b/bin/X86MAC64/mrcImateToPointsSet
index a4ac408..44e07a0 100755 (executable)
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diff --git a/bin/X86MAC64/mrcInfo b/bin/X86MAC64/mrcInfo
index 13956d4..30aa8e5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcInfoSet b/bin/X86MAC64/mrcInfoSet
index 3b554ea..4c8033b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcMask b/bin/X86MAC64/mrcMask
index e0ef8a3..7bc1ade 100755 (executable)
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diff --git a/bin/X86MAC64/mrcMeanYlinePos b/bin/X86MAC64/mrcMeanYlinePos
index 95d0159..c1b1ca8 100755 (executable)
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diff --git a/bin/X86MAC64/mrcMirrorImageCreate b/bin/X86MAC64/mrcMirrorImageCreate
index 974fbe1..eb13b75 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRadon2Dto3D b/bin/X86MAC64/mrcRadon2Dto3D
index 0fba0d9..32d6f10 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefCorEstimate b/bin/X86MAC64/mrcRefCorEstimate
index 8c4d34d..63cc672 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefCorModify b/bin/X86MAC64/mrcRefCorModify
index bdb027c..b2d4c3d 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefCoreGet b/bin/X86MAC64/mrcRefCoreGet
index 4553252..9c2c387 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefCorrelation b/bin/X86MAC64/mrcRefCorrelation
index ffc7cda..dc47ee5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefCorrelationConv b/bin/X86MAC64/mrcRefCorrelationConv
index 9aefab1..8c2d972 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefEstimate b/bin/X86MAC64/mrcRefEstimate
index 9f6288f..a849145 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefFFTConvert b/bin/X86MAC64/mrcRefFFTConvert
index 1f467ab..8d2cbb1 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefHeaderCreate b/bin/X86MAC64/mrcRefHeaderCreate
index e021265..8659ab5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefHighPassFilter b/bin/X86MAC64/mrcRefHighPassFilter
index 166561f..bbb01d4 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImageCorrelation b/bin/X86MAC64/mrcRefImageCorrelation
index ffeb2bc..4c3d383 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImageOmegaCorrelation b/bin/X86MAC64/mrcRefImageOmegaCorrelation
index 5426a9e..09c3847 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImagepwzCorEstimate b/bin/X86MAC64/mrcRefImagepwzCorEstimate
index 8fc525e..2f57524 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImagepwzCorModify b/bin/X86MAC64/mrcRefImagepwzCorModify
index bbc4647..17c909f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImagepwzCorPeakFind b/bin/X86MAC64/mrcRefImagepwzCorPeakFind
index 557c436..0c804a7 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImagepwzCorSmoothing b/bin/X86MAC64/mrcRefImagepwzCorSmoothing
index c2ee1cf..0a78a5a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImagepwzCorrelation b/bin/X86MAC64/mrcRefImagepwzCorrelation
index 8e6fd76..c050af3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImagepwzCorrelationByFFT b/bin/X86MAC64/mrcRefImagepwzCorrelationByFFT
index d433956..3921e2a 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefImagexaFit b/bin/X86MAC64/mrcRefImagexaFit
index 0d1cd88..2d5569f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefLowPassFilter b/bin/X86MAC64/mrcRefLowPassFilter
index cbfdb26..3a6daad 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefNoiseAdd b/bin/X86MAC64/mrcRefNoiseAdd
index 441e2a2..6896efc 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefNormalizing b/bin/X86MAC64/mrcRefNormalizing
index 586df12..5e4ebf3 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefPhaseImageCreate b/bin/X86MAC64/mrcRefPhaseImageCreate
index 6237856..0aaafbd 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefSmoothing b/bin/X86MAC64/mrcRefSmoothing
index 44a3600..539a36f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcRefz1ImageCorrelation b/bin/X86MAC64/mrcRefz1ImageCorrelation
index 1a37eab..0b2f80b 100755 (executable)
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diff --git a/bin/X86MAC64/mrcSinogramFET b/bin/X86MAC64/mrcSinogramFET
index ffa2805..ba4acb5 100755 (executable)
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diff --git a/bin/X86MAC64/mrcSinogramFETcalcSDforNormalize b/bin/X86MAC64/mrcSinogramFETcalcSDforNormalize
index 23de16e..d22fa6f 100755 (executable)
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diff --git a/bin/X86MAC64/mrcSinogramFETcalcWeight b/bin/X86MAC64/mrcSinogramFETcalcWeight
index 036405c..7c2c66e 100755 (executable)
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diff --git a/bin/X86MAC64/mrcSinogramFETcorrelationMap b/bin/X86MAC64/mrcSinogramFETcorrelationMap
index dea487e..c0e5044 100755 (executable)
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diff --git a/bin/X86MAC64/mrcSinogramFETnormalizedMap b/bin/X86MAC64/mrcSinogramFETnormalizedMap
index de3b63d..d935781 100755 (executable)
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diff --git a/bin/X86MAC64/mrcSinogramFETreferredCorrelation b/bin/X86MAC64/mrcSinogramFETreferredCorrelation
index da285c2..d63e496 100755 (executable)
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diff --git a/bin/X86MAC64/mrcSinogramFETsmoothParameterMatching b/bin/X86MAC64/mrcSinogramFETsmoothParameterMatching
index f4affcf..de93ffb 100755 (executable)
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diff --git a/bin/X86MAC64/pdb2SketchMacro b/bin/X86MAC64/pdb2SketchMacro
index 6d62290..1223abb 100755 (executable)
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diff --git a/bin/X86MAC64/pdb2bender b/bin/X86MAC64/pdb2bender
index 5426a9e..09c3847 100755 (executable)
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diff --git a/bin/X86MAC64/pdb2mrc b/bin/X86MAC64/pdb2mrc
index cca8834..da66e49 100755 (executable)
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diff --git a/bin/X86MAC64/pdb2mrc2d b/bin/X86MAC64/pdb2mrc2d
index a646e40..937ba2c 100755 (executable)
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diff --git a/bin/X86MAC64/pdb2ucd b/bin/X86MAC64/pdb2ucd
index e54c283..6f67db1 100755 (executable)
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diff --git a/bin/X86MAC64/pdbAtomSection b/bin/X86MAC64/pdbAtomSection
index 79b13e6..ff8250f 100755 (executable)
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diff --git a/bin/X86MAC64/pdbCAOnly b/bin/X86MAC64/pdbCAOnly
index 182741d..d872ac4 100755 (executable)
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diff --git a/bin/X86MAC64/pdbChargeFit b/bin/X86MAC64/pdbChargeFit
index 6a10841..fb58611 100755 (executable)
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diff --git a/bin/X86MAC64/pdbCoordAdd b/bin/X86MAC64/pdbCoordAdd
index d265f41..5365657 100755 (executable)
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diff --git a/bin/X86MAC64/pdbCrystalCreate b/bin/X86MAC64/pdbCrystalCreate
index a530949..67364a7 100755 (executable)
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diff --git a/bin/X86MAC64/pdbDisplay b/bin/X86MAC64/pdbDisplay
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diff --git a/bin/X86MAC64/pdbFileMerge b/bin/X86MAC64/pdbFileMerge
index 27d10ac..a3b49d6 100755 (executable)
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diff --git a/bin/X86MAC64/pdbHelix b/bin/X86MAC64/pdbHelix
index 5b5ca5f..cb81221 100755 (executable)
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index 8850f27..fa3823e 100644 (file)
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diff --git a/lib/X86MAC64/shared/randomUniform.sharedo b/lib/X86MAC64/shared/randomUniform.sharedo
index 995da68..9292875 100644 (file)
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diff --git a/lib/X86MAC64/shared/savePPM.sharedo b/lib/X86MAC64/shared/savePPM.sharedo
new file mode 100644 (file)
index 0000000..6b03cfa
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diff --git a/lib/X86MAC64/shared/socketClient.sharedo b/lib/X86MAC64/shared/socketClient.sharedo
index d104d39..95ab711 100644 (file)
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diff --git a/lib/X86MAC64/shared/socketServer.sharedo b/lib/X86MAC64/shared/socketServer.sharedo
index 42e7ab4..24a68d5 100644 (file)
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diff --git a/lib/X86MAC64/shared/srandom.sharedo b/lib/X86MAC64/shared/srandom.sharedo
index 11ca2c0..667d77f 100644 (file)
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diff --git a/lib/X86MAC64/shared/stringGet.sharedo b/lib/X86MAC64/shared/stringGet.sharedo
index d6558c3..286f1f0 100644 (file)
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diff --git a/lib/X86MAC64/shared/stringGetFromFile.sharedo b/lib/X86MAC64/shared/stringGetFromFile.sharedo
index 409f21e..657eb03 100644 (file)
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diff --git a/lib/X86MAC64/shared/stringIsSame.sharedo b/lib/X86MAC64/shared/stringIsSame.sharedo
index 3884118..a0f4d52 100644 (file)
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diff --git a/lib/X86MAC64/shared/stringUtil.sharedo b/lib/X86MAC64/shared/stringUtil.sharedo
index 006124c..b4e0e92 100644 (file)
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diff --git a/lib/X86MAC64/shared/tgaFileInit.sharedo b/lib/X86MAC64/shared/tgaFileInit.sharedo
index f2fc426..7190be4 100644 (file)
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diff --git a/lib/X86MAC64/shared/tgaFilePrint.sharedo b/lib/X86MAC64/shared/tgaFilePrint.sharedo
index d05d355..989c6be 100644 (file)
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diff --git a/lib/X86MAC64/shared/tgaFileRead.sharedo b/lib/X86MAC64/shared/tgaFileRead.sharedo
index 47214e4..62d95a3 100644 (file)
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diff --git a/lib/X86MAC64/shared/thonRing.sharedo b/lib/X86MAC64/shared/thonRing.sharedo
index e1a621d..132dd70 100644 (file)
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diff --git a/lib/X86MAC64/shared/tkImgFmtMRC.sharedo b/lib/X86MAC64/shared/tkImgFmtMRC.sharedo
index 8d8ceb4..9651c63 100755 (executable)
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diff --git a/lib/X86MAC64/shared/tkImgFmtlargeIP.sharedo b/lib/X86MAC64/shared/tkImgFmtlargeIP.sharedo
index 4800376..06459db 100755 (executable)
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diff --git a/lib/X86MAC64/shared/tkctfInfo.sharedo b/lib/X86MAC64/shared/tkctfInfo.sharedo
index 485f85e..ba2800b 100644 (file)
Binary files a/lib/X86MAC64/shared/tkctfInfo.sharedo and b/lib/X86MAC64/shared/tkctfInfo.sharedo differ

diff --git a/src/Objects/DataExpress/Contour/src/X86MAC64/.Depend b/src/Objects/DataExpress/Contour/src/X86MAC64/.Depend
index 05a34a5..83a3e1c 100644 (file)
--- a/src/Objects/DataExpress/Contour/src/X86MAC64/.Depend
+++ b/src/Objects/DataExpress/Contour/src/X86MAC64/.Depend
@@ -1,72 +1,3 @@
-contourCreate.o: contourCreate.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/Contour.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lcontour2ps.o: lcontour2ps.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/psFile.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/Contour.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrc2contour.o: lmrc2contour.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/Contour.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+X86MAC64/contourCreate.o:contourCreate.o
+X86MAC64/lcontour2ps.o:lcontour2ps.o
+X86MAC64/lmrc2contour.o:lmrc2contour.o

diff --git a/src/Objects/DataExpress/Contour/src/X86MAC64/contourCreate.sharedo b/src/Objects/DataExpress/Contour/src/X86MAC64/contourCreate.sharedo
index 0ef3c24..fdc4d30 100644 (file)
Binary files a/src/Objects/DataExpress/Contour/src/X86MAC64/contourCreate.sharedo and b/src/Objects/DataExpress/Contour/src/X86MAC64/contourCreate.sharedo differ

diff --git a/src/Objects/DataExpress/Contour/src/X86MAC64/lcontour2ps.sharedo b/src/Objects/DataExpress/Contour/src/X86MAC64/lcontour2ps.sharedo
index 956f5f5..a56c972 100644 (file)
Binary files a/src/Objects/DataExpress/Contour/src/X86MAC64/lcontour2ps.sharedo and b/src/Objects/DataExpress/Contour/src/X86MAC64/lcontour2ps.sharedo differ

diff --git a/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.a b/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.a
index d649d6e..70d5bea 100644 (file)
Binary files a/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.a and b/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.a differ

diff --git a/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.debug.a b/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.debug.a
index 4be28fb..fb6a7b8 100644 (file)
Binary files a/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.debug.a and b/src/Objects/DataExpress/Contour/src/X86MAC64/libContour.debug.a differ

diff --git a/src/Objects/DataExpress/Contour/src/X86MAC64/lmrc2contour.sharedo b/src/Objects/DataExpress/Contour/src/X86MAC64/lmrc2contour.sharedo
index f57501d..503e39f 100644 (file)
Binary files a/src/Objects/DataExpress/Contour/src/X86MAC64/lmrc2contour.sharedo and b/src/Objects/DataExpress/Contour/src/X86MAC64/lmrc2contour.sharedo differ

diff --git a/src/Objects/DataExpress/TclTk/src/X86MAC64/.Depend b/src/Objects/DataExpress/TclTk/src/X86MAC64/.Depend
index af2e8f8..3414406 100644 (file)
--- a/src/Objects/DataExpress/TclTk/src/X86MAC64/.Depend
+++ b/src/Objects/DataExpress/TclTk/src/X86MAC64/.Depend
@@ -1,107 +1,3 @@
-tkImgFmtMRC.o: tkImgFmtMRC.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h tkImgFmtMRC.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/X11/X.h /usr/include/X11/Xfuncproto.h \
-  /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/alloca.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/string.h
-tkImgFmtlargeIP.o: tkImgFmtlargeIP.c \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
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-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
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-  /usr/include/sys/appleapiopts.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/X11/X.h /usr/include/X11/Xfuncproto.h \
-  /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/largeIP.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/alloca.h
-tkctfInfo.o: tkctfInfo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h tkctfInfo.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/ctfZeroPoint.h
+X86MAC64/tkImgFmtMRC.o:tkImgFmtMRC.o
+X86MAC64/tkImgFmtlargeIP.o:tkImgFmtlargeIP.o
+X86MAC64/tkctfInfo.o:tkctfInfo.o

diff --git a/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.a b/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.a
index e182990..1d140c7 100644 (file)
Binary files a/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.a and b/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.a differ

diff --git a/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.debug.a b/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.debug.a
index 862df65..169e70a 100644 (file)
Binary files a/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.debug.a and b/src/Objects/DataExpress/TclTk/src/X86MAC64/libTclTk.debug.a differ

diff --git a/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtMRC.sharedo b/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtMRC.sharedo
index 8d8ceb4..9651c63 100644 (file)
Binary files a/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtMRC.sharedo and b/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtMRC.sharedo differ

diff --git a/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtlargeIP.sharedo b/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtlargeIP.sharedo
index 4800376..06459db 100644 (file)
Binary files a/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtlargeIP.sharedo and b/src/Objects/DataExpress/TclTk/src/X86MAC64/tkImgFmtlargeIP.sharedo differ

diff --git a/src/Objects/DataExpress/TclTk/src/X86MAC64/tkctfInfo.sharedo b/src/Objects/DataExpress/TclTk/src/X86MAC64/tkctfInfo.sharedo
index 485f85e..ba2800b 100644 (file)
Binary files a/src/Objects/DataExpress/TclTk/src/X86MAC64/tkctfInfo.sharedo and b/src/Objects/DataExpress/TclTk/src/X86MAC64/tkctfInfo.sharedo differ

diff --git a/src/Objects/DataExpress/alsa/src/X86MAC64/.Depend b/src/Objects/DataExpress/alsa/src/X86MAC64/.Depend
index 6a6e733..49056a4 100644 (file)
--- a/src/Objects/DataExpress/alsa/src/X86MAC64/.Depend
+++ b/src/Objects/DataExpress/alsa/src/X86MAC64/.Depend
@@ -1,4 +1 @@
-monoSound.o: monoSound.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h
+X86MAC64/monoSound.o:monoSound.o

diff --git a/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.a b/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.a
index 6fbd0d5..cf9cfad 100644 (file)
Binary files a/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.a and b/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.a differ

diff --git a/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.debug.a b/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.debug.a
index cfea297..f7bb648 100644 (file)
Binary files a/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.debug.a and b/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.debug.a differ

diff --git a/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.so b/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.so
index e6b912f..091b9af 100755 (executable)
Binary files a/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.so and b/src/Objects/DataExpress/alsa/src/X86MAC64/libalsa.so differ

diff --git a/src/Objects/DataExpress/avsFile/src/X86MAC64/.Depend b/src/Objects/DataExpress/avsFile/src/X86MAC64/.Depend
index 01d6b3a..b6c52c9 100644 (file)
--- a/src/Objects/DataExpress/avsFile/src/X86MAC64/.Depend
+++ b/src/Objects/DataExpress/avsFile/src/X86MAC64/.Depend
@@ -1,78 +1,3 @@
-avsFileInit.o: avsFileInit.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/avsFile.h
-avsFileSet.o: avsFileSet.c /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/avsFile.h
-avsFileWrite.o: avsFileWrite.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/avsFile.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
+X86MAC64/avsFileInit.o:avsFileInit.o
+X86MAC64/avsFileSet.o:avsFileSet.o
+X86MAC64/avsFileWrite.o:avsFileWrite.o

diff --git a/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileInit.sharedo b/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileInit.sharedo
index 6c578a5..bab41b7 100644 (file)
Binary files a/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileInit.sharedo and b/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileInit.sharedo differ

diff --git a/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileSet.sharedo b/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileSet.sharedo
index 08a017f..a505689 100644 (file)
Binary files a/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileSet.sharedo and b/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileSet.sharedo differ

diff --git a/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileWrite.sharedo b/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileWrite.sharedo
index 5983eaf..7f316e9 100644 (file)
Binary files a/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileWrite.sharedo and b/src/Objects/DataExpress/avsFile/src/X86MAC64/avsFileWrite.sharedo differ

diff --git a/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.a b/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.a
index 653f31f..01ed98b 100644 (file)
Binary files a/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.a and b/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.a differ

diff --git a/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.debug.a b/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.debug.a
index 584969d..101692e 100644 (file)
Binary files a/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.debug.a and b/src/Objects/DataExpress/avsFile/src/X86MAC64/libavsFile.debug.a differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/.Depend b/src/Objects/DataExpress/gifFile/src/X86MAC64/.Depend
index b52bcca..98b3847 100644 (file)
--- a/src/Objects/DataExpress/gifFile/src/X86MAC64/.Depend
+++ b/src/Objects/DataExpress/gifFile/src/X86MAC64/.Depend
@@ -1,143 +1,7 @@
-decoder.o: decoder.c ../inc/gifFile.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/gif_lib.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-gifFileInit.o: gifFileInit.c ../inc/gifFile.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/gif_lib.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
-gifFileWrite.o: gifFileWrite.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/gifFile.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/gif_lib.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
-gifUtil.o: gifUtil.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/gifFile.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/gif_lib.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
-gifcompr.o: gifcompr.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/ctype.h \
-  /usr/include/runetype.h /usr/include/signal.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h
-gifencod.o: gifencod.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-lmrc2gif.o: lmrc2gif.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/gifFile.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/gif_lib.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+X86MAC64/decoder.o:decoder.o
+X86MAC64/gifFileInit.o:gifFileInit.o
+X86MAC64/gifFileWrite.o:gifFileWrite.o
+X86MAC64/gifUtil.o:gifUtil.o
+X86MAC64/gifcompr.o:gifcompr.o
+X86MAC64/gifencod.o:gifencod.o
+X86MAC64/lmrc2gif.o:lmrc2gif.o

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/decoder.sharedo b/src/Objects/DataExpress/gifFile/src/X86MAC64/decoder.sharedo
index 8429532..f76d0bb 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/decoder.sharedo and b/src/Objects/DataExpress/gifFile/src/X86MAC64/decoder.sharedo differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileInit.sharedo b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileInit.sharedo
index 028d09b..7730b14 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileInit.sharedo and b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileInit.sharedo differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileWrite.sharedo b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileWrite.sharedo
index c439dcb..8fb8d03 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileWrite.sharedo and b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifFileWrite.sharedo differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifUtil.sharedo b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifUtil.sharedo
index 2d0a5fb..9787a67 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifUtil.sharedo and b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifUtil.sharedo differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifencod.sharedo b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifencod.sharedo
index 81502dc..c4b6696 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/gifencod.sharedo and b/src/Objects/DataExpress/gifFile/src/X86MAC64/gifencod.sharedo differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.a b/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.a
index e941068..2313bd6 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.a and b/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.a differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.debug.a b/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.debug.a
index 4d84b81..d8ac728 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.debug.a and b/src/Objects/DataExpress/gifFile/src/X86MAC64/libgifFile.debug.a differ

diff --git a/src/Objects/DataExpress/gifFile/src/X86MAC64/lmrc2gif.sharedo b/src/Objects/DataExpress/gifFile/src/X86MAC64/lmrc2gif.sharedo
index 62f6a9b..e63d4f3 100644 (file)
Binary files a/src/Objects/DataExpress/gifFile/src/X86MAC64/lmrc2gif.sharedo and b/src/Objects/DataExpress/gifFile/src/X86MAC64/lmrc2gif.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/.Depend b/src/Objects/DataExpress/openGL/src/X86MAC64/.Depend
index d18534b..ebae8dc 100644 (file)
--- a/src/Objects/DataExpress/openGL/src/X86MAC64/.Depend
+++ b/src/Objects/DataExpress/openGL/src/X86MAC64/.Depend
@@ -1,54 +1,52 @@
-lmolvieMRCread.o: lmolvieMRCread.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmolviePDBread.o: lmolviePDBread.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-openGLKey.o: openGLKey.c ../inc/openGL.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h
+X86MAC64/density_sphere.o:density_sphere.o
+X86MAC64/drawWireFrame.o:drawWireFrame.o
+X86MAC64/lmolvieCamera.o:lmolvieCamera.o
+X86MAC64/lmolvieDisplayLib.o:lmolvieDisplayLib.o
+X86MAC64/lmolvieDisplayListMake.o:lmolvieDisplayListMake.o
+X86MAC64/lmolvieDisplayNormal.o:lmolvieDisplayNormal.o
+X86MAC64/lmolvieDisplayParallel.o:lmolvieDisplayParallel.o
+X86MAC64/lmolvieDockDisplay.o:lmolvieDockDisplay.o
+X86MAC64/lmolvieDockKeyboard.o:lmolvieDockKeyboard.o
+X86MAC64/lmolvieFlightDisplay.o:lmolvieFlightDisplay.o
+X86MAC64/lmolvieFlightIdle.o:lmolvieFlightIdle.o
+X86MAC64/lmolvieFlightKeyboard.o:lmolvieFlightKeyboard.o
+X86MAC64/lmolvieIdleNormal.o:lmolvieIdleNormal.o
+X86MAC64/lmolvieInitNormal.o:lmolvieInitNormal.o
+X86MAC64/lmolvieInitParallel.o:lmolvieInitParallel.o
+X86MAC64/lmolvieKeyboard.o:lmolvieKeyboard.o
+X86MAC64/lmolvieKeyboardDrive.o:lmolvieKeyboardDrive.o
+X86MAC64/lmolvieKeyboardMulti.o:lmolvieKeyboardMulti.o
+X86MAC64/lmolvieKeyboardNormal.o:lmolvieKeyboardNormal.o
+X86MAC64/lmolvieKeyboardParallel.o:lmolvieKeyboardParallel.o
+X86MAC64/lmolvieKeyboardSurface.o:lmolvieKeyboardSurface.o
+X86MAC64/lmolvieLight.o:lmolvieLight.o
+X86MAC64/lmolvieMRCread.o:lmolvieMRCread.o
+X86MAC64/lmolvieMouse.o:lmolvieMouse.o
+X86MAC64/lmolvieMouseDrive.o:lmolvieMouseDrive.o
+X86MAC64/lmolvieMouseMulti.o:lmolvieMouseMulti.o
+X86MAC64/lmolvieMouseNormal.o:lmolvieMouseNormal.o
+X86MAC64/lmolvieMouseParallel.o:lmolvieMouseParallel.o
+X86MAC64/lmolvieMrcViewerDisplay.o:lmolvieMrcViewerDisplay.o
+X86MAC64/lmolvieMrcViewerKeyboard.o:lmolvieMrcViewerKeyboard.o
+X86MAC64/lmolvieMrcViewerMouse.o:lmolvieMrcViewerMouse.o
+X86MAC64/lmolvieOperation.o:lmolvieOperation.o
+X86MAC64/lmolviePDBread.o:lmolviePDBread.o
+X86MAC64/lmolvieProjectionKeyboard.o:lmolvieProjectionKeyboard.o
+X86MAC64/lmolvieProjectionMouse.o:lmolvieProjectionMouse.o
+X86MAC64/lmolvieProteinStatus.o:lmolvieProteinStatus.o
+X86MAC64/lmolvieReshapeNormal.o:lmolvieReshapeNormal.o
+X86MAC64/lmolvieReshapeParallel.o:lmolvieReshapeParallel.o
+X86MAC64/lmolvieTest.o:lmolvieTest.o
+X86MAC64/lmolvieTexture.o:lmolvieTexture.o
+X86MAC64/lmolvieViewerDisplay.o:lmolvieViewerDisplay.o
+X86MAC64/lmolvieViewerIdle.o:lmolvieViewerIdle.o
+X86MAC64/lmolvieViewerKeyboard.o:lmolvieViewerKeyboard.o
+X86MAC64/lmolvieViewerMouse.o:lmolvieViewerMouse.o
+X86MAC64/lmolvieViewerSpecial.o:lmolvieViewerSpecial.o
+X86MAC64/lmolvieVoice.o:lmolvieVoice.o
+X86MAC64/loadPDB.o:loadPDB.o
+X86MAC64/loadPPM.o:loadPPM.o
+X86MAC64/marching_cubes.o:marching_cubes.o
+X86MAC64/multiPDB.o:multiPDB.o
+X86MAC64/openGLKey.o:openGLKey.o
+X86MAC64/savePPM.o:savePPM.o

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/density_sphere.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/density_sphere.sharedo
new file mode 100644 (file)
index 0000000..bad14d5
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/density_sphere.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/drawWireFrame.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/drawWireFrame.sharedo
new file mode 100644 (file)
index 0000000..b602f48
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/drawWireFrame.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.a b/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.a
index 55f39cf..09576a4 100644 (file)
Binary files a/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.a and b/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.a differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.debug.a b/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.debug.a
index 3d47184..83e5b54 100644 (file)
Binary files a/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.debug.a and b/src/Objects/DataExpress/openGL/src/X86MAC64/libopenGL.debug.a differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieCamera.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieCamera.sharedo
new file mode 100644 (file)
index 0000000..2b2a975
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieCamera.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayLib.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayLib.sharedo
new file mode 100644 (file)
index 0000000..199b1b7
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayLib.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayListMake.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayListMake.sharedo
new file mode 100644 (file)
index 0000000..221a5a3
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayListMake.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayNormal.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayNormal.sharedo
new file mode 100644 (file)
index 0000000..9980d3b
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayNormal.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayParallel.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayParallel.sharedo
new file mode 100644 (file)
index 0000000..7af8602
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDisplayParallel.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDockDisplay.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDockDisplay.sharedo
new file mode 100644 (file)
index 0000000..f22c7e6
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDockDisplay.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDockKeyboard.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDockKeyboard.sharedo
new file mode 100644 (file)
index 0000000..823fe39
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieDockKeyboard.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightDisplay.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightDisplay.sharedo
new file mode 100644 (file)
index 0000000..f387d3b
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightDisplay.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightIdle.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightIdle.sharedo
new file mode 100644 (file)
index 0000000..1a31647
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightIdle.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightKeyboard.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightKeyboard.sharedo
new file mode 100644 (file)
index 0000000..afb7fce
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieFlightKeyboard.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieIdleNormal.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieIdleNormal.sharedo
new file mode 100644 (file)
index 0000000..3fa0388
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieIdleNormal.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieInitNormal.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieInitNormal.sharedo
new file mode 100644 (file)
index 0000000..7bd08cf
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieInitNormal.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieInitParallel.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieInitParallel.sharedo
new file mode 100644 (file)
index 0000000..40342bb
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieInitParallel.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboard.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboard.sharedo
new file mode 100644 (file)
index 0000000..3759bcf
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboard.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardDrive.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardDrive.sharedo
new file mode 100644 (file)
index 0000000..5dd4590
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardDrive.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardMulti.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardMulti.sharedo
new file mode 100644 (file)
index 0000000..31d0211
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardMulti.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardNormal.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardNormal.sharedo
new file mode 100644 (file)
index 0000000..4f05bb4
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardNormal.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardParallel.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardParallel.sharedo
new file mode 100644 (file)
index 0000000..f723fa8
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardParallel.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardSurface.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardSurface.sharedo
new file mode 100644 (file)
index 0000000..f6d86c4
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieKeyboardSurface.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieLight.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieLight.sharedo
new file mode 100644 (file)
index 0000000..dcde6cf
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieLight.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMRCread.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMRCread.sharedo
index fa585a4..80087d9 100644 (file)
Binary files a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMRCread.sharedo and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMRCread.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouse.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouse.sharedo
new file mode 100644 (file)
index 0000000..bf58b7f
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouse.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseDrive.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseDrive.sharedo
new file mode 100644 (file)
index 0000000..77fd3c8
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseDrive.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseMulti.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseMulti.sharedo
new file mode 100644 (file)
index 0000000..8733fd1
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseMulti.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseNormal.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseNormal.sharedo
new file mode 100644 (file)
index 0000000..8b10fa5
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseNormal.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseParallel.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseParallel.sharedo
new file mode 100644 (file)
index 0000000..c3b02c7
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMouseParallel.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerDisplay.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerDisplay.sharedo
new file mode 100644 (file)
index 0000000..7d2824f
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerDisplay.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerKeyboard.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerKeyboard.sharedo
new file mode 100644 (file)
index 0000000..e631ea2
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerKeyboard.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerMouse.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerMouse.sharedo
new file mode 100644 (file)
index 0000000..b45de57
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieMrcViewerMouse.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieOperation.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieOperation.sharedo
new file mode 100644 (file)
index 0000000..3ffe197
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieOperation.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolviePDBread.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolviePDBread.sharedo
index 46dbb36..9a3aede 100644 (file)
Binary files a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolviePDBread.sharedo and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolviePDBread.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProjectionKeyboard.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProjectionKeyboard.sharedo
new file mode 100644 (file)
index 0000000..7901ddb
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProjectionKeyboard.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProjectionMouse.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProjectionMouse.sharedo
new file mode 100644 (file)
index 0000000..181b104
Binary files /dev/null and b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProjectionMouse.sharedo differ

diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProteinStatus.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieProteinStatus.sharedo
new file mode 100644 (file)
index 0000000..3ac7b42
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieReshapeParallel.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieReshapeParallel.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieTexture.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieTexture.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerDisplay.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerDisplay.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerIdle.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerIdle.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerKeyboard.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerKeyboard.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerMouse.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerMouse.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerSpecial.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/lmolvieViewerSpecial.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/loadPDB.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/loadPDB.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/openGLKey.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/openGLKey.sharedo
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diff --git a/src/Objects/DataExpress/openGL/src/X86MAC64/savePPM.sharedo b/src/Objects/DataExpress/openGL/src/X86MAC64/savePPM.sharedo
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diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/.Depend b/src/Objects/DataExpress/psFile/src/X86MAC64/.Depend
index 8f26d6a..f79fbb1 100644 (file)
--- a/src/Objects/DataExpress/psFile/src/X86MAC64/.Depend
+++ b/src/Objects/DataExpress/psFile/src/X86MAC64/.Depend
@@ -1,231 +1,11 @@
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-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h ../inc/psFile.h \
-  /Applications/Eos.app/Eos/include/File.h
+X86MAC64/psFileCircle.o:psFileCircle.o
+X86MAC64/psFileContour.o:psFileContour.o
+X86MAC64/psFileContour3D.o:psFileContour3D.o
+X86MAC64/psFileEnd.o:psFileEnd.o
+X86MAC64/psFileImage.o:psFileImage.o
+X86MAC64/psFileInit.o:psFileInit.o
+X86MAC64/psFileLine.o:psFileLine.o
+X86MAC64/psFilePage.o:psFilePage.o
+X86MAC64/psFileRead.o:psFileRead.o
+X86MAC64/psFileString.o:psFileString.o
+X86MAC64/psFileUtil.o:psFileUtil.o

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.a b/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.a
index 9a12a5d..6965453 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.a and b/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.a differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.debug.a b/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.debug.a
index afb9c72..33daef4 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.debug.a and b/src/Objects/DataExpress/psFile/src/X86MAC64/libpsFile.debug.a differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileCircle.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileCircle.sharedo
index 27ec33c..ce427ad 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileCircle.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileCircle.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour.sharedo
index 6357572..4eed924 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour3D.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour3D.sharedo
index f69b7ec..59aefab 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour3D.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileContour3D.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileEnd.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileEnd.sharedo
index ea93381..0bcd2c5 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileEnd.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileEnd.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileImage.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileImage.sharedo
index c13bf92..ea8618b 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileImage.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileImage.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileInit.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileInit.sharedo
index 09c6b9a..628bbcf 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileInit.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileInit.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileLine.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileLine.sharedo
index 530763d..19b1b86 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileLine.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileLine.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFilePage.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFilePage.sharedo
index 3caf59c..ac07568 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFilePage.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFilePage.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileRead.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileRead.sharedo
index 9dde5e6..670b0a8 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileRead.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileRead.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileString.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileString.sharedo
index a2606fc..149d94b 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileString.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileString.sharedo differ

diff --git a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileUtil.sharedo b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileUtil.sharedo
index 4aa7305..557eff9 100644 (file)
Binary files a/src/Objects/DataExpress/psFile/src/X86MAC64/psFileUtil.sharedo and b/src/Objects/DataExpress/psFile/src/X86MAC64/psFileUtil.sharedo differ

diff --git a/src/Objects/DataManip/DCDFile/src/X86MAC64/.Depend b/src/Objects/DataManip/DCDFile/src/X86MAC64/.Depend
index 717169d..f3f445e 100644 (file)
--- a/src/Objects/DataManip/DCDFile/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/DCDFile/src/X86MAC64/.Depend
@@ -1,103 +1 @@
-dcd.o: dcd.cc ../inc/DCDFile.h /usr/include/c++/4.2.1/iostream \
-  /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/unistd.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/sys/select.h /usr/include/sys/appleapiopts.h \
-  /usr/include/sys/_structs.h /usr/include/sys/_select.h \
-  /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdio.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+X86MAC64/dcd.o:dcd.o

diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/.Depend b/src/Objects/DataManip/MATH/src/X86MAC64/.Depend
index 1d262fb..15428d3 100644 (file)
--- a/src/Objects/DataManip/MATH/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/MATH/src/X86MAC64/.Depend
@@ -1,156 +1,19 @@
-10.1.o: 10.1.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h nr2.h
-10.2.o: 10.2.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h nr2.h
-10.5.o: 10.5.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h nr2.h
-10.6.o: 10.6.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h nr2.h
-10.7.o: 10.7.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h nr2.h
-11.1.o: 11.1.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h nr2.h
-13.10.o: 13.10.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h nr2.h
-15.2.o: 15.2.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h nr2.h
-15.4.o: 15.4.c
-15.5.o: 15.5.c nr2.h
-15.7.o: 15.7.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h nr2.h
-2.1.o: 2.1.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h nr2.h
-2.3.o: 2.3.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h nr2.h
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-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-8.2.o: 8.2.c nr2.h
-8.5.o: 8.5.c nr2.h
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-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
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-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
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-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h nr2.h
+X86MAC64/10.1.o:10.1.o
+X86MAC64/10.2.o:10.2.o
+X86MAC64/10.5.o:10.5.o
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+X86MAC64/11.1.o:11.1.o
+X86MAC64/13.10.o:13.10.o
+X86MAC64/15.2.o:15.2.o
+X86MAC64/15.4.o:15.4.o
+X86MAC64/15.5.o:15.5.o
+X86MAC64/15.7.o:15.7.o
+X86MAC64/2.1.o:2.1.o
+X86MAC64/2.3.o:2.3.o
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+X86MAC64/6.4.o:6.4.o
+X86MAC64/8.2.o:8.2.o
+X86MAC64/8.5.o:8.5.o
+X86MAC64/nr2util.o:nr2util.o

diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/10.1.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/10.1.sharedo
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/15.4.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/15.4.sharedo
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/15.5.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/15.5.sharedo
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/6.1.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/6.1.sharedo
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/6.2.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/6.2.sharedo
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/6.4.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/6.4.sharedo
index f83421a..3128c97 100644 (file)
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/8.2.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/8.2.sharedo
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/libMATH.a b/src/Objects/DataManip/MATH/src/X86MAC64/libMATH.a
index a8976f6..be8733d 100644 (file)
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/libMATH.debug.a b/src/Objects/DataManip/MATH/src/X86MAC64/libMATH.debug.a
index ecba6b4..9e61949 100644 (file)
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diff --git a/src/Objects/DataManip/MATH/src/X86MAC64/nr2util.sharedo b/src/Objects/DataManip/MATH/src/X86MAC64/nr2util.sharedo
index f7d2ad4..2458284 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/.Depend b/src/Objects/DataManip/ctfInfo/src/X86MAC64/.Depend
index 5f8d04a..8ece161 100644 (file)
--- a/src/Objects/DataManip/ctfInfo/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/ctfInfo/src/X86MAC64/.Depend
@@ -1,372 +1,15 @@
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- ctfDeterminationFromPhaseComparison.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
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-  /Applications/Eos.app/Eos/include/ctfInfo.h \
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-  /Applications/Eos.app/Eos/include/Matrix3D.h \
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-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
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-ctfWeight.o: ctfWeight.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
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-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Vector.h ../inc/ctfInfo.h
-ctfZeroPoint.o: ctfZeroPoint.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Vector.h ../inc/ctfInfo.h \
-  ctfZeroPoint.h
-lastigmatismDetection.o: lastigmatismDetection.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  lastigmatismDetection.h ../inc/ctfInfo.h
-lctfDetermination.o: lctfDetermination.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h lctfDetermination.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/ctfInfo.h \
-  powerspectraTangentLine.h lctfDetermination.h ctfInfoWrite2.h \
-  lmrcFSInfoScatteringAngularDistributionAverageSection.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/nr2.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lctfDetermine.o: lctfDetermine.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcFSInfoScatteringAngularDistributionAverageSection.h \
-  lctfDetermination.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  ../inc/ctfInfo.h lastigmatismDetection.h
-lmolecularEnvelope.o: lmolecularEnvelope.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h ../inc/ctfInfo.h
-lmrcFSInfoScatteringAngularDistributionAverageSection.o:  \
- lmrcFSInfoScatteringAngularDistributionAverageSection.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  lmrcFSInfoScatteringAngularDistributionAverageSection.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/Vector.h
-powerspectraTangentLine.o: powerspectraTangentLine.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  powerspectraTangentLine.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/ctfInfo.h \
-  lctfDetermination.h ctfInfoWrite2.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/nr2.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-thonRing.o: thonRing.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h
+X86MAC64/ctfDeterminationFromPhaseComparison.o:ctfDeterminationFromPhaseComparison.o
+X86MAC64/ctfFunction.o:ctfFunction.o
+X86MAC64/ctfInfoPVM.o:ctfInfoPVM.o
+X86MAC64/ctfInfoRead.o:ctfInfoRead.o
+X86MAC64/ctfInfoWrite.o:ctfInfoWrite.o
+X86MAC64/ctfInfoWrite2.o:ctfInfoWrite2.o
+X86MAC64/ctfWeight.o:ctfWeight.o
+X86MAC64/ctfZeroPoint.o:ctfZeroPoint.o
+X86MAC64/lastigmatismDetection.o:lastigmatismDetection.o
+X86MAC64/lctfDetermination.o:lctfDetermination.o
+X86MAC64/lctfDetermine.o:lctfDetermine.o
+X86MAC64/lmolecularEnvelope.o:lmolecularEnvelope.o
+X86MAC64/lmrcFSInfoScatteringAngularDistributionAverageSection.o:lmrcFSInfoScatteringAngularDistributionAverageSection.o
+X86MAC64/powerspectraTangentLine.o:powerspectraTangentLine.o
+X86MAC64/thonRing.o:thonRing.o

diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfDeterminationFromPhaseComparison.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfDeterminationFromPhaseComparison.sharedo
index d91f43a..237b129 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfFunction.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfFunction.sharedo
index a9d051f..1f98a0d 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfInfoRead.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfInfoRead.sharedo
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfInfoWrite.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfInfoWrite.sharedo
index 7479711..c344795 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfInfoWrite2.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfInfoWrite2.sharedo
index 4bb72cb..e664767 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfWeight.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfWeight.sharedo
index 8d33551..3c78c89 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfZeroPoint.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/ctfZeroPoint.sharedo
index f7f79f1..5b8b2ba 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/lastigmatismDetection.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/lastigmatismDetection.sharedo
index 3f8e90b..328e6e9 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/lctfDetermination.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/lctfDetermination.sharedo
index 4691ae7..529295a 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/lctfDetermine.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/lctfDetermine.sharedo
index 30806be..4182468 100644 (file)
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diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.a b/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.a
index 12a1060..e1a8133 100644 (file)
Binary files a/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.a and b/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.a differ

diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.debug.a b/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.debug.a
index cf356c7..4fd0b13 100644 (file)
Binary files a/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.debug.a and b/src/Objects/DataManip/ctfInfo/src/X86MAC64/libctfInfo.debug.a differ

diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmolecularEnvelope.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmolecularEnvelope.sharedo
index 7d3b7ef..88e4614 100644 (file)
Binary files a/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmolecularEnvelope.sharedo and b/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmolecularEnvelope.sharedo differ

diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmrcFSInfoScatteringAngularDistributionAverageSection.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmrcFSInfoScatteringAngularDistributionAverageSection.sharedo
index 3f5a041..29c75a4 100644 (file)
Binary files a/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmrcFSInfoScatteringAngularDistributionAverageSection.sharedo and b/src/Objects/DataManip/ctfInfo/src/X86MAC64/lmrcFSInfoScatteringAngularDistributionAverageSection.sharedo differ

diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/powerspectraTangentLine.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/powerspectraTangentLine.sharedo
index d171c35..52efe06 100644 (file)
Binary files a/src/Objects/DataManip/ctfInfo/src/X86MAC64/powerspectraTangentLine.sharedo and b/src/Objects/DataManip/ctfInfo/src/X86MAC64/powerspectraTangentLine.sharedo differ

diff --git a/src/Objects/DataManip/ctfInfo/src/X86MAC64/thonRing.sharedo b/src/Objects/DataManip/ctfInfo/src/X86MAC64/thonRing.sharedo
index e1a621d..132dd70 100644 (file)
Binary files a/src/Objects/DataManip/ctfInfo/src/X86MAC64/thonRing.sharedo and b/src/Objects/DataManip/ctfInfo/src/X86MAC64/thonRing.sharedo differ

diff --git a/src/Objects/DataManip/dsn6File/src/X86MAC64/.Depend b/src/Objects/DataManip/dsn6File/src/X86MAC64/.Depend
index 3a44d67..6a32a7d 100644 (file)
--- a/src/Objects/DataManip/dsn6File/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/dsn6File/src/X86MAC64/.Depend
@@ -1,34 +1,2 @@
-dsn6Init.o: dsn6Init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/dsn6File.h
-dsn6Write.o: dsn6Write.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/dsn6File.h
+X86MAC64/dsn6Init.o:dsn6Init.o
+X86MAC64/dsn6Write.o:dsn6Write.o

diff --git a/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Init.sharedo b/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Init.sharedo
index c0cfec2..24f164f 100644 (file)
Binary files a/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Init.sharedo and b/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Init.sharedo differ

diff --git a/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Write.sharedo b/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Write.sharedo
index 2dea089..862802c 100644 (file)
Binary files a/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Write.sharedo and b/src/Objects/DataManip/dsn6File/src/X86MAC64/dsn6Write.sharedo differ

diff --git a/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.a b/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.a
index 3160fc7..7adab7c 100644 (file)
Binary files a/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.a and b/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.a differ

diff --git a/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.debug.a b/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.debug.a
index 440afdb..4383e43 100644 (file)
Binary files a/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.debug.a and b/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.debug.a differ

diff --git a/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.so b/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.so
index b8109ed..c5abb32 100755 (executable)
Binary files a/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.so and b/src/Objects/DataManip/dsn6File/src/X86MAC64/libdsn6File.so differ

diff --git a/src/Objects/DataManip/emData/src/X86MAC64/.Depend b/src/Objects/DataManip/emData/src/X86MAC64/.Depend
index 655eb3c..91d68b7 100644 (file)
--- a/src/Objects/DataManip/emData/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/emData/src/X86MAC64/.Depend
@@ -1,26 +1 @@
-emDataRead.o: emDataRead.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/emData.h
+X86MAC64/emDataRead.o:emDataRead.o

diff --git a/src/Objects/DataManip/emData/src/X86MAC64/emDataRead.sharedo b/src/Objects/DataManip/emData/src/X86MAC64/emDataRead.sharedo
index 8dc8a94..92d99b8 100644 (file)
Binary files a/src/Objects/DataManip/emData/src/X86MAC64/emDataRead.sharedo and b/src/Objects/DataManip/emData/src/X86MAC64/emDataRead.sharedo differ

diff --git a/src/Objects/DataManip/emData/src/X86MAC64/libemData.a b/src/Objects/DataManip/emData/src/X86MAC64/libemData.a
index f3d6681..3e4bfa7 100644 (file)
Binary files a/src/Objects/DataManip/emData/src/X86MAC64/libemData.a and b/src/Objects/DataManip/emData/src/X86MAC64/libemData.a differ

diff --git a/src/Objects/DataManip/emData/src/X86MAC64/libemData.debug.a b/src/Objects/DataManip/emData/src/X86MAC64/libemData.debug.a
index d1388d3..17015fc 100644 (file)
Binary files a/src/Objects/DataManip/emData/src/X86MAC64/libemData.debug.a and b/src/Objects/DataManip/emData/src/X86MAC64/libemData.debug.a differ

diff --git a/src/Objects/DataManip/khorosData/src/X86MAC64/.Depend b/src/Objects/DataManip/khorosData/src/X86MAC64/.Depend
index e69de29..ffcf632 100644 (file)
--- a/src/Objects/DataManip/khorosData/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/khorosData/src/X86MAC64/.Depend
@@ -0,0 +1 @@
+X86MAC64/lmrc2viff.o:lmrc2viff.o

diff --git a/src/Objects/DataManip/largeIP/src/X86MAC64/.Depend b/src/Objects/DataManip/largeIP/src/X86MAC64/.Depend
index 8a6ce13..37b0b64 100644 (file)
--- a/src/Objects/DataManip/largeIP/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/largeIP/src/X86MAC64/.Depend
@@ -1,17 +1,2 @@
-largeIPRead.o: largeIPRead.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/largeIP.h
+X86MAC64/largeIPRead.o:largeIPRead.o
+X86MAC64/tkImgFmtlargeIP.o:tkImgFmtlargeIP.o

diff --git a/src/Objects/DataManip/largeIP/src/X86MAC64/largeIPRead.sharedo b/src/Objects/DataManip/largeIP/src/X86MAC64/largeIPRead.sharedo
index ea5db9c..b6f85df 100644 (file)
Binary files a/src/Objects/DataManip/largeIP/src/X86MAC64/largeIPRead.sharedo and b/src/Objects/DataManip/largeIP/src/X86MAC64/largeIPRead.sharedo differ

diff --git a/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.a b/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.a
index 5f9adb1..52dc149 100644 (file)
Binary files a/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.a and b/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.a differ

diff --git a/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.debug.a b/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.debug.a
index 1ecfddd..5e47c04 100644 (file)
Binary files a/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.debug.a and b/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.debug.a differ

diff --git a/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.so b/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.so
index 878ba77..f50f62a 100755 (executable)
Binary files a/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.so and b/src/Objects/DataManip/largeIP/src/X86MAC64/liblargeIP.so differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/.Depend b/src/Objects/DataManip/llData/src/X86MAC64/.Depend
index 6c9cc32..9c1fc71 100644 (file)
--- a/src/Objects/DataManip/llData/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/llData/src/X86MAC64/.Depend
@@ -1,909 +1,44 @@
-llDataCheck.o: llDataCheck.c ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-llDataETC.o: llDataETC.c ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-llDataError.o: llDataError.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h ../inc/llData.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-llDataGet.o: llDataGet.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-llDataInfo.o: llDataInfo.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-llDataInit.o: llDataInit.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-llDataIntensityInformationGet.o: llDataIntensityInformationGet.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-llDataPVM.o: llDataPVM.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-llDataRead.o: llDataRead.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-llDataSet.o: llDataSet.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-llDataUtil.o: llDataUtil.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-llDataWrite.o: llDataWrite.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lll2ltlg.o: lll2ltlg.c lll2ltlg.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/ltlgData.h
-lllDataAdd.o: lllDataAdd.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lllDataAverage.o: lllDataAverage.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lllDataFitAndAverage.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataCTFCompensation.h
-lllDataAvgTo.o: lllDataAvgTo.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lllDataAxisSearch.o: lllDataAxisSearch.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataAxisSearch.h \
-  ../inc/llData.h lllDataFit.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataAxisSearch2.o: lllDataAxisSearch2.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/nr2.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  ../inc/llData.h /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataAxisSearchAndAverage.o: lllDataAxisSearchAndAverage.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lllDataAxisSearch.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataCTFCompensate.o: lllDataCTFCompensate.c lllDataCTFCompensate.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/File.h
-lllDataCTFObservation.o: lllDataCTFObservation.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataCompare.o: lllDataCompare.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataCompare.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h
-lllDataContributionCalcDifferentN.o: lllDataContributionCalcDifferentN.c \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
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-lllDataDifferenceCalc.o: lllDataDifferenceCalc.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h lllDataDifferenceCalc.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h
-lllDataEquatorAdd.o: lllDataEquatorAdd.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataEquatorAdd.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h
-lllDataExtract.o: lllDataExtract.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataExtract.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h
-lllDataFit.o: lllDataFit.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/llData.h /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  ../inc/llData.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lllDataFit2.o: lllDataFit2.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  ../inc/llData.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/nr2.h
-lllDataFitAndAverage.o: lllDataFitAndAverage.c /usr/include/unistd.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/unistd.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/sys/select.h /usr/include/sys/appleapiopts.h \
-  /usr/include/sys/_structs.h /usr/include/sys/_select.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
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-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/File.h \
-  lllDataFitAndAverage.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataCTFCompensation.h
-lllDataFitMergedLL.o: lllDataFitMergedLL.c ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataFitOut.o: lllDataFitOut.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  ../inc/llData.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lllDataFitParamInverse.o: lllDataFitParamInverse.c ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  ../inc/llData.h /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataFitUtil.o: lllDataFitUtil.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  lllDataFit.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataFitUtilPVM.o: lllDataFitUtilPVM.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/llData.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  lllDataFit.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
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-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lllDataInterpolate.o: lllDataInterpolate.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lllDataLowPassFiltering.o: lllDataLowPassFiltering.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lllDataLowPassFiltering.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataMergeDifferentN.o: lllDataMergeDifferentN.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h lllDataMergeDifferentN.h
-lllDataMultiCTFCompensation.o: lllDataMultiCTFCompensation.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFitAndAverage.h \
-  lllDataFit.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  lllDataCTFCompensation.h
-lllDataPhaseShift.o: lllDataPhaseShift.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataFit.h \
-  ../inc/llData.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  lllDataFitParamInverse.h
-lllDataPrint.o: lllDataPrint.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/psFile.h \
-  /Applications/Eos.app/Eos/include/File.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  ../inc/llData.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lllDataRescaling.o: lllDataRescaling.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataRescaling.h \
-  ../inc/llData.h
-lllDataSingleCTFCompensation.o: lllDataSingleCTFCompensation.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lllDataCTFCompensation.h \
-  lllDataFit.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  lllDataFitAndAverage.h
-lllDataWeightSet.o: lllDataWeightSet.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/llData.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/String.h
-lllDatarMaxLimit.o: lllDatarMaxLimit.c ../inc/llData.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lllDatarMaxLimit.h
+X86MAC64/llDataCheck.o:llDataCheck.o
+X86MAC64/llDataETC.o:llDataETC.o
+X86MAC64/llDataError.o:llDataError.o
+X86MAC64/llDataGet.o:llDataGet.o
+X86MAC64/llDataInfo.o:llDataInfo.o
+X86MAC64/llDataInit.o:llDataInit.o
+X86MAC64/llDataIntensityInformationGet.o:llDataIntensityInformationGet.o
+X86MAC64/llDataPVM.o:llDataPVM.o
+X86MAC64/llDataRead.o:llDataRead.o
+X86MAC64/llDataSet.o:llDataSet.o
+X86MAC64/llDataUtil.o:llDataUtil.o
+X86MAC64/llDataWrite.o:llDataWrite.o
+X86MAC64/lll2ltlg.o:lll2ltlg.o
+X86MAC64/lllDataAdd.o:lllDataAdd.o
+X86MAC64/lllDataAverage.o:lllDataAverage.o
+X86MAC64/lllDataAvgTo.o:lllDataAvgTo.o
+X86MAC64/lllDataAxisSearch.o:lllDataAxisSearch.o
+X86MAC64/lllDataAxisSearch2.o:lllDataAxisSearch2.o
+X86MAC64/lllDataAxisSearchAndAverage.o:lllDataAxisSearchAndAverage.o
+X86MAC64/lllDataCTFCompensate.o:lllDataCTFCompensate.o
+X86MAC64/lllDataCTFObservation.o:lllDataCTFObservation.o
+X86MAC64/lllDataCompare.o:lllDataCompare.o
+X86MAC64/lllDataContributionCalcDifferentN.o:lllDataContributionCalcDifferentN.o
+X86MAC64/lllDataDifferenceCalc.o:lllDataDifferenceCalc.o
+X86MAC64/lllDataEquatorAdd.o:lllDataEquatorAdd.o
+X86MAC64/lllDataExtract.o:lllDataExtract.o
+X86MAC64/lllDataFit.o:lllDataFit.o
+X86MAC64/lllDataFit2.o:lllDataFit2.o
+X86MAC64/lllDataFitAndAverage.o:lllDataFitAndAverage.o
+X86MAC64/lllDataFitMergedLL.o:lllDataFitMergedLL.o
+X86MAC64/lllDataFitOut.o:lllDataFitOut.o
+X86MAC64/lllDataFitParamInverse.o:lllDataFitParamInverse.o
+X86MAC64/lllDataFitUtil.o:lllDataFitUtil.o
+X86MAC64/lllDataFitUtilPVM.o:lllDataFitUtilPVM.o
+X86MAC64/lllDataInterpolate.o:lllDataInterpolate.o
+X86MAC64/lllDataLowPassFiltering.o:lllDataLowPassFiltering.o
+X86MAC64/lllDataMergeDifferentN.o:lllDataMergeDifferentN.o
+X86MAC64/lllDataMultiCTFCompensation.o:lllDataMultiCTFCompensation.o
+X86MAC64/lllDataPhaseShift.o:lllDataPhaseShift.o
+X86MAC64/lllDataPrint.o:lllDataPrint.o
+X86MAC64/lllDataRescaling.o:lllDataRescaling.o
+X86MAC64/lllDataSingleCTFCompensation.o:lllDataSingleCTFCompensation.o
+X86MAC64/lllDataWeightSet.o:lllDataWeightSet.o
+X86MAC64/lllDatarMaxLimit.o:lllDatarMaxLimit.o

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/libllData.a b/src/Objects/DataManip/llData/src/X86MAC64/libllData.a
index 5156f56..331a7fe 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/libllData.a and b/src/Objects/DataManip/llData/src/X86MAC64/libllData.a differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/libllData.debug.a b/src/Objects/DataManip/llData/src/X86MAC64/libllData.debug.a
index 33bdefa..be59792 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/libllData.debug.a and b/src/Objects/DataManip/llData/src/X86MAC64/libllData.debug.a differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataCheck.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataCheck.sharedo
index e3402e8..734c99c 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/llDataCheck.sharedo and b/src/Objects/DataManip/llData/src/X86MAC64/llDataCheck.sharedo differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataETC.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataETC.sharedo
index a3319cd..879a294 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/llDataETC.sharedo and b/src/Objects/DataManip/llData/src/X86MAC64/llDataETC.sharedo differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataError.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataError.sharedo
index 33056b6..7c2b6d2 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/llDataError.sharedo and b/src/Objects/DataManip/llData/src/X86MAC64/llDataError.sharedo differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataGet.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataGet.sharedo
index b289081..48652bf 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/llDataGet.sharedo and b/src/Objects/DataManip/llData/src/X86MAC64/llDataGet.sharedo differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataInfo.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataInfo.sharedo
index ce50580..d7d92e5 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/llDataInfo.sharedo and b/src/Objects/DataManip/llData/src/X86MAC64/llDataInfo.sharedo differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataInit.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataInit.sharedo
index a0ba3f8..8328297 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/llDataInit.sharedo and b/src/Objects/DataManip/llData/src/X86MAC64/llDataInit.sharedo differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataIntensityInformationGet.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataIntensityInformationGet.sharedo
index fa6c27d..00da3f5 100644 (file)
Binary files a/src/Objects/DataManip/llData/src/X86MAC64/llDataIntensityInformationGet.sharedo and b/src/Objects/DataManip/llData/src/X86MAC64/llDataIntensityInformationGet.sharedo differ

diff --git a/src/Objects/DataManip/llData/src/X86MAC64/llDataRead.sharedo b/src/Objects/DataManip/llData/src/X86MAC64/llDataRead.sharedo
index eaaa994..a53281e 100644 (file)
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diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/.Depend b/src/Objects/DataManip/ltlgData/src/X86MAC64/.Depend
index 4127bef..9cf37f6 100644 (file)
--- a/src/Objects/DataManip/ltlgData/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/ltlgData/src/X86MAC64/.Depend
@@ -1,160 +1,7 @@
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-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/ltlgData.h
-ltlgDataWeightModify.o: ltlgDataWeightModify.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/ltlgData.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h
-ltlgDataWriteFile.o: ltlgDataWriteFile.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/ltlgData.h
+X86MAC64/lltlg2mrc.o:lltlg2mrc.o
+X86MAC64/ltlgDataAllocate.o:ltlgDataAllocate.o
+X86MAC64/ltlgDataGet.o:ltlgDataGet.o
+X86MAC64/ltlgDataPrint.o:ltlgDataPrint.o
+X86MAC64/ltlgDataReadFile.o:ltlgDataReadFile.o
+X86MAC64/ltlgDataWeightModify.o:ltlgDataWeightModify.o
+X86MAC64/ltlgDataWriteFile.o:ltlgDataWriteFile.o

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.a b/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.a
index a52eb2b..856e4dc 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.a and b/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.a differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.debug.a b/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.debug.a
index 6c4ec25..407dae3 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.debug.a and b/src/Objects/DataManip/ltlgData/src/X86MAC64/libltlgData.debug.a differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/lltlg2mrc.sharedo b/src/Objects/DataManip/ltlgData/src/X86MAC64/lltlg2mrc.sharedo
index c52be39..f9120c7 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/lltlg2mrc.sharedo and b/src/Objects/DataManip/ltlgData/src/X86MAC64/lltlg2mrc.sharedo differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataAllocate.sharedo b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataAllocate.sharedo
index 91a5d1d..9e7a00b 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataAllocate.sharedo and b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataAllocate.sharedo differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataGet.sharedo b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataGet.sharedo
index 417b924..f6e7779 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataGet.sharedo and b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataGet.sharedo differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataPrint.sharedo b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataPrint.sharedo
index 125b273..98d517f 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataPrint.sharedo and b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataPrint.sharedo differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataReadFile.sharedo b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataReadFile.sharedo
index 81580bd..a763863 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataReadFile.sharedo and b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataReadFile.sharedo differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWeightModify.sharedo b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWeightModify.sharedo
index 85d7ffc..e3a220c 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWeightModify.sharedo and b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWeightModify.sharedo differ

diff --git a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWriteFile.sharedo b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWriteFile.sharedo
index d0c5d5e..d216729 100644 (file)
Binary files a/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWriteFile.sharedo and b/src/Objects/DataManip/ltlgData/src/X86MAC64/ltlgDataWriteFile.sharedo differ

diff --git a/src/Objects/DataManip/mapFile/src/X86MAC64/.Depend b/src/Objects/DataManip/mapFile/src/X86MAC64/.Depend
index c6ffd92..cfbe32f 100644 (file)
--- a/src/Objects/DataManip/mapFile/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/mapFile/src/X86MAC64/.Depend
@@ -1,7 +1 @@
-mapFileRead.o: mapFileRead.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h ../inc/mapFile.h
+X86MAC64/mapFileRead.o:mapFileRead.o

diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/.Depend b/src/Objects/DataManip/mrcImage/src/X86MAC64/.Depend
index 3cf416a..a12ec2a 100644 (file)
--- a/src/Objects/DataManip/mrcImage/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/mrcImage/src/X86MAC64/.Depend
@@ -1,3730 +1,146 @@
-fftn.o: fftn.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h fftn.h fftn.c
-lmrcFETnormalizeBySD.o: lmrcFETnormalizeBySD.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcFETnormalizeBySD.h \
-  ../inc/mrcImage.h
-lmrcFFTExpression.o: lmrcFFTExpression.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcFFTExpression.h \
-  ../inc/mrcImage.h
-lmrcFFTFGconj.o: lmrcFFTFGconj.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lmrcFFTFxG.o: lmrcFFTFxG.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lmrcFFTInfo.o: lmrcFFTInfo.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/Vector.h \
-  lmrcFFTInfo.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/Vector.h
-lmrcImage3DWindowing.o: lmrcImage3DWindowing.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImage3DWindowing.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageAddValue.o: lmrcImageAddValue.c lmrcImageAddValue.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageAsProbability.o: lmrcImageAsProbability.c \
-  lmrcImageAsProbability.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageAverage.o: lmrcImageAverage.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageAverage.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageBandPassFilter.o: lmrcImageBandPassFilter.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lmrcImageBilateralFilter.o: lmrcImageBilateralFilter.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageBilateralFilter.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageBinarization.o: lmrcImageBinarization.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageBinarization.h \
-  ../inc/mrcImage.h
-lmrcImageBoundaryInfo.o: lmrcImageBoundaryInfo.c lmrcImageBoundaryInfo.h
-lmrcImageCTFCompensation.o: lmrcImageCTFCompensation.c \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lmrcImageCTFDetermination.o: lmrcImageCTFDetermination.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  lmrcImageCTFDetermination.h /Applications/Eos.app/Eos/include/ctfInfo.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lllDataCTFCompensate.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/lll2ltlg.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/ltlgData.h \
-  /Applications/Eos.app/Eos/include/lltlg2mrc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  lmrcImageSolventFlattening.h \
-  /Applications/Eos.app/Eos/include/genUtil.h lmrcImageProjection.h \
-  lmrcImageCrystalCreate.h \
-  /Applications/Eos.app/Eos/include/lllExtractdYEstimate.h lmrcImagePad.h \
-  /Applications/Eos.app/Eos/include/Memory.h
-lmrcImageCTFObservation.o: lmrcImageCTFObservation.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lmrcImageCTFSN.o: lmrcImageCTFSN.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-lmrcImageCVE.o: lmrcImageCVE.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lmrcImageCalcArea.o: lmrcImageCalcArea.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageLabeling.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageCalcArea.h
-lmrcImageCenterGet.o: lmrcImageCenterGet.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/Random.h \
-  /usr/include/time.h
-lmrcImageCentre.o: lmrcImageCentre.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageCentre.h
-lmrcImageClosing.o: lmrcImageClosing.c lmrcImageMorphology.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageClusterAnalysis.o: lmrcImageClusterAnalysis.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h lmrcImageClusterAnalysis.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/nr2.h \
-  /Applications/Eos.app/Eos/include/mrcRefUtil.h lmrcImageMultiplying.h \
-  lmrcImageCorrelation.h /Applications/Eos.app/Eos/include/PVM.h \
-  lmrcImageSSDA.h /Applications/Eos.app/Eos/include/Cluster.h
-lmrcImageCommonLine.o: lmrcImageCommonLine.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImageSinogram.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageCommonLine.h \
-  lmrcImageCentre.h /usr/include/stdlib.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lmrcImageConnection.o: lmrcImageConnection.c lmrcImageConnection.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageConnectivityNumberCalc.o: lmrcImageConnectivityNumberCalc.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageConnectivityNumberCalc.h ../inc/mrcImage.h
-lmrcImageContourSurface.o: lmrcImageContourSurface.c \
-  lmrcImageContourSurface.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageContraction.o: lmrcImageContraction.c
-lmrcImageCorrelation.o: lmrcImageCorrelation.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageCorrelation.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/PVM.h \
-  lmrcImageSSDA.h /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
-  lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/Map2D.h
-lmrcImageCorrelationPVM.o: lmrcImageCorrelationPVM.c
-lmrcImageCorrelationWithCTFCompensation.o:  \
- lmrcImageCorrelationWithCTFCompensation.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageCorrelationinSpace.o: lmrcImageCorrelationinSpace.c \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcRefUtil.h
-lmrcImageCrystalCreate.o: lmrcImageCrystalCreate.c \
-  lmrcImageCrystalCreate.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageDataMaxAndMinGetByImage.o: lmrcImageDataMaxAndMinGetByImage.c \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageDataMaxAndMinGetByImage.h
-lmrcImageDataStraightCopy.o: lmrcImageDataStraightCopy.c \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageDataStraightCopy.h
-lmrcImageDensity.o: lmrcImageDensity.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageModeChange.h \
-  /Applications/Eos.app/Eos/include/Vector.h lmrcImageDensity.h
-lmrcImageDensityInverse.o: lmrcImageDensityInverse.c \
-  lmrcImageDensityInverse.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageDensityNormalizationByImage.o:  \
- lmrcImageDensityNormalizationByImage.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/nr2.h \
-  lmrcImageDensityNormalizationByImage.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageSummationCalculate.h \
-  lmrcImageStudentCalculate.h
-lmrcImageDilation.o: lmrcImageDilation.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageMorphology.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h
-lmrcImageDistanceConversion.o: lmrcImageDistanceConversion.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageDistanceConversion.h \
-  ../inc/mrcImage.h lmrcImageConnectivityNumberCalc.h
-lmrcImageEdge.o: lmrcImageEdge.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageEdge.h ../inc/mrcImage.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageEdgeAverage.o: lmrcImageEdgeAverage.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageEdgeAverage.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageErosion.o: lmrcImageErosion.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageMorphology.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h
-lmrcImageFFT.o: lmrcImageFFT.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h \
-  /Applications/Eos.app/Eos/include/eosPThread.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/fftw3.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h
-lmrcImageFOMCalc.o: lmrcImageFOMCalc.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageFOMCalc.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageFeatureExtraction.o: lmrcImageFeatureExtraction.c \
-  lmrcImageFeatureExtraction.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h
-lmrcImageFeatureExtractionCoOccurrence.o:  \
- lmrcImageFeatureExtractionCoOccurrence.c lmrcImageFeatureExtraction.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImagePosterization.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/nr2.h
-lmrcImageFeatureExtractionRunLength.o:  \
- lmrcImageFeatureExtractionRunLength.c lmrcImageFeatureExtraction.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImagePosterization.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/nr2.h \
-  ../inc/mrcImage.h
-lmrcImageFilterCreate.o: lmrcImageFilterCreate.c \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/String.h \
-  lmrcImageFilterCreate.h ../inc/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageFirstNoiseReductionByRelaxation.o:  \
- lmrcImageFirstNoiseReductionByRelaxation.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  lmrcImagePixelSummationOfProbabilityGetByImage.h
-lmrcImageFourierPowerSpectrum.o: lmrcImageFourierPowerSpectrum.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-lmrcImageFourierShellCorrelation.o: lmrcImageFourierShellCorrelation.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageFourierShellCorrelation.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/./mrcRefUtil.h
-lmrcImageHighPassFilter.o: lmrcImageHighPassFilter.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lmrcImageHighlighting.o: lmrcImageHighlighting.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lmrcImageLabeling.o: lmrcImageLabeling.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImageLabeling.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageLowPassFilter.o: lmrcImageLowPassFilter.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lmrcImageMasking.o: lmrcImageMasking.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageMasking.h
-lmrcImageMaxDataGet.o: lmrcImageMaxDataGet.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageMirroring.o: lmrcImageMirroring.c lmrcImageMirroring.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageModeChange.o: lmrcImageModeChange.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageModeChange.h
-lmrcImageModelCreate.o: lmrcImageModelCreate.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageModelCreate.h
-lmrcImageMontageCreate.o: lmrcImageMontageCreate.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageMontage.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImagePad.h \
-  /Applications/Eos.app/Eos/include/string.h lmrcImageEdgeAverage.h
-lmrcImageMorphology.o: lmrcImageMorphology.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h lmrcImageMorphology.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageMove.o: lmrcImageMove.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageMove.h ../inc/mrcImage.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
-lmrcImageMultiCTFCompensation.o: lmrcImageMultiCTFCompensation.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h lmrcImageCTFCompensation.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-lmrcImageMultiplying.o: lmrcImageMultiplying.c lmrcImageMultiplying.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageNormalizing.o: lmrcImageNormalizing.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/nr2.h lmrcImageNormalizing.h
-lmrcImageOneLineSimilarityCalc.o: lmrcImageOneLineSimilarityCalc.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageOneLineSimilarityCalc.h ../inc/mrcImage.h
-lmrcImageOpening.o: lmrcImageOpening.c lmrcImageMorphology.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImagePad.o: lmrcImagePad.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImagePad.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h lmrcImageCalcArea.h lmrcImageTriming.h \
-  lmrcImageBinarization.h lmrcImageEdge.h
-lmrcImagePartImageSegmentation.o: lmrcImagePartImageSegmentation.c \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImagePixelSummationOfProbabilityGetByImage.o:  \
- lmrcImagePixelSummationOfProbabilityGetByImage.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  lmrcImagePixelSummationOfProbabilityGetByImage.h
-lmrcImagePosterization.o: lmrcImagePosterization.c \
-  lmrcImageFeatureExtraction.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImagePosterization.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h
-lmrcImageProjection.o: lmrcImageProjection.c lmrcImageProjection.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageProportionalDensityLevelSetByImage.o:  \
- lmrcImageProportionalDensityLevelSetByImage.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  lmrcImageProportionalDensityLevelSetByImage.h
-lmrcImageROI2D.o: lmrcImageROI2D.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h lmrcImageROI2D.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageROI3D.o: lmrcImageROI3D.c lmrcImageROI3D.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageROInotChangeHeaderLength.o: lmrcImageROInotChangeHeaderLength.c \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcRefUtil.h
-lmrcImageRadialDistribution.o: lmrcImageRadialDistribution.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageRadialDistribution.h \
-  /Applications/Eos.app/Eos/include/Vector.h
-lmrcImageRhoFiltering.o: lmrcImageRhoFiltering.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h lmrcImageRhoFiltering.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/Matrix3D.h
-lmrcImageRotation.o: lmrcImageRotation.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
-lmrcImageSSDA.o: lmrcImageSSDA.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImageSSDA.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSamplingUnitChange.o: lmrcImageSamplingUnitChange.c \
-  lmrcImageSamplingUnitChange.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSecondNoiseReductionByRelaxation.o:  \
- lmrcImageSecondNoiseReductionByRelaxation.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  lmrcImageSecondNoiseReductionByRelaxation.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h
-lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.o:  \
- lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.c \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.o:  \
- lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.c \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.h
-lmrcImageSecondNoiseReductionByRelaxationDijValueSet.o:  \
- lmrcImageSecondNoiseReductionByRelaxationDijValueSet.c \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxationDijValueSet.h \
-  lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.h
-lmrcImageSecondNoiseReductionByRelaxationQValueSet.o:  \
- lmrcImageSecondNoiseReductionByRelaxationQValueSet.c \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxationQValueSet.h
-lmrcImageSecondNoiseReductionByRelaxationRValueSet.o:  \
- lmrcImageSecondNoiseReductionByRelaxationRValueSet.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageFirstNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxation.h \
-  lmrcImageSecondNoiseReductionByRelaxationRValueSet.h
-lmrcImageShapePCA.o: lmrcImageShapePCA.c lmrcImageShapePCA.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageShift.o: lmrcImageShift.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  lmrcImageDensity.h /usr/include/stdlib.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h lmrcImageModeChange.h \
-  /Applications/Eos.app/Eos/include/Vector.h
-lmrcImageShrink.o: lmrcImageShrink.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  ../inc/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lmrcImageSigmaCalculate.o: lmrcImageSigmaCalculate.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImageSummationCalculate.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageSigmaCalculate.h
-lmrcImageSinogram.o: lmrcImageSinogram.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImageSinogram.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageBinarization.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-lmrcImageSinogramCorrelation.o: lmrcImageSinogramCorrelation.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h lmrcImageSinogram.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageBinarization.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-lmrcImageSinogramFFT.o: lmrcImageSinogramFFT.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSmoothing.o: lmrcImageSmoothing.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSolventFlattening.o: lmrcImageSolventFlattening.c \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageSolventFlattening.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h
-lmrcImageSphere.o: lmrcImageSphere.c lmrcImageSphere.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSplit.o: lmrcImageSplit.c \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImageSplit.h ../inc/mrcImage.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageStudentCalculate.o: lmrcImageStudentCalculate.c \
-  lmrcImageStudentCalculate.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSubtractionCalc.o: lmrcImageSubtractionCalc.c \
-  lmrcImageSubtractionCalc.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSummationCalculate.o: lmrcImageSummationCalculate.c \
-  lmrcImageSummationCalculate.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageSymmetryFind.o: lmrcImageSymmetryFind.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcRefUtil.h \
-  lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
-  lmrcImageSymmetryFind.h /Applications/Eos.app/Eos/include/Vector.h \
-  lmrcImageSubtractionCalc.h lmrcImagesStatDataGet.h lmrcFFTExpression.h
-lmrcImageTfunction.o: lmrcImageTfunction.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-lmrcImageTrans.o: lmrcImageTrans.c ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h
-lmrcImageTransformDescartesIntoPolar.o:  \
- lmrcImageTransformDescartesIntoPolar.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageCentre.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/./lDescartesIntoPolar.h \
-  lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h
-lmrcImageTriming.o: lmrcImageTriming.c lmrcImageTriming.h \
-  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageVolumeCalc.o: lmrcImageVolumeCalc.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/nr2.h \
-  lmrcImageVolumeCalc.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImageWindowing.o: lmrcImageWindowing.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcImageWindowing.h
-lmrcImagesFTest.o: lmrcImagesFTest.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/nr2.h \
-  lmrcImagesStatDataGet.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImagesStatDataGet.o: lmrcImagesStatDataGet.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h lmrcImagesStatDataGet.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImagesTTest.o: lmrcImagesTTest.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/nr2.h \
-  lmrcImagesStatDataGet.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImagesVarianceAnalysis.o: lmrcImagesVarianceAnalysis.c \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/nr2.h \
-  lmrcImagesStatDataGet.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcImagesVarianceMap.o: lmrcImagesVarianceMap.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/nr2.h \
-  lmrcImagesStatDataGet.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-lmrcSinogramFET.o: lmrcSinogramFET.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcSinogramFET.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/Array.h \
-  lmrcImageBinarization.h lmrcImagePosterization.h
-lmrcSinogramFETPCA.o: lmrcSinogramFETPCA.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcSinogramFET.h \
-  ../inc/mrcImage.h
-lmrcSinogramFETcalcWeight.o: lmrcSinogramFETcalcWeight.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  lmrcSinogramFETcalcWeight.h /usr/include/math.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcSinogramFET.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/nr2.h
-lmrcSinogramFETcorrelationMap.o: lmrcSinogramFETcorrelationMap.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcSinogramFET.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/Array.h \
-  lmrcSinogramFETcorrelationMap.h
-lmrcSinogramFETnormalizedMap.o: lmrcSinogramFETnormalizedMap.c \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcSinogramFET.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/Array.h \
-  lmrcSinogramFETnormalizedMap.h lmrcImageBinarization.h
-lmrcSinogramFETreferredCorrelation.o:  \
- lmrcSinogramFETreferredCorrelation.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcSinogramFET.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/Array.h \
-  lmrcSinogramFETreferredCorrelation.h
-lmrcSinogramFETsmoothParameterMatching.o:  \
- lmrcSinogramFETsmoothParameterMatching.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h lmrcSinogramFET.h \
-  ../inc/mrcImage.h /Applications/Eos.app/Eos/include/Array.h \
-  lmrcSinogramFETsmoothParameterMatching.h
-mrcImageCheckFFT.o: mrcImageCheckFFT.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImageCheckSameSize.o: mrcImageCheckSameSize.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImageCopy.o: mrcImageCopy.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImageDataSet.o: mrcImageDataSet.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImageError.o: mrcImageError.c ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-mrcImageGet.o: mrcImageGet.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-mrcImageInfo.o: mrcImageInfo.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-mrcImageInit.o: mrcImageInit.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImageOperation.o: mrcImageOperation.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImagePVM.o: mrcImagePVM.c
-mrcImagePrint.o: mrcImagePrint.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h /usr/include/time.h \
-  /usr/include/_structs.h lmrcImagePrint.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/psFile.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/Contour.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
-mrcImageRead.o: mrcImageRead.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lmrcImagePrint.h ../inc/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/psFile.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/mrcImage.h
-mrcImageSectionGet.o: mrcImageSectionGet.c \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImageSectionSet.o: mrcImageSectionSet.c ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-mrcImageSet.o: mrcImageSet.c /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/mrcImage.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h
-mrcImageTailer.o: mrcImageTailer.c \
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+X86MAC64/lmrcImagesVarianceAnalysis.o:lmrcImagesVarianceAnalysis.o
+X86MAC64/lmrcImagesVarianceMap.o:lmrcImagesVarianceMap.o
+X86MAC64/lmrcSinogramFET.o:lmrcSinogramFET.o
+X86MAC64/lmrcSinogramFETPCA.o:lmrcSinogramFETPCA.o
+X86MAC64/lmrcSinogramFETcalcWeight.o:lmrcSinogramFETcalcWeight.o
+X86MAC64/lmrcSinogramFETcorrelationMap.o:lmrcSinogramFETcorrelationMap.o
+X86MAC64/lmrcSinogramFETnormalizedMap.o:lmrcSinogramFETnormalizedMap.o
+X86MAC64/lmrcSinogramFETreferredCorrelation.o:lmrcSinogramFETreferredCorrelation.o
+X86MAC64/lmrcSinogramFETsmoothParameterMatching.o:lmrcSinogramFETsmoothParameterMatching.o
+X86MAC64/mrcImageCheckFFT.o:mrcImageCheckFFT.o
+X86MAC64/mrcImageCheckSameSize.o:mrcImageCheckSameSize.o
+X86MAC64/mrcImageCopy.o:mrcImageCopy.o
+X86MAC64/mrcImageDataSet.o:mrcImageDataSet.o
+X86MAC64/mrcImageError.o:mrcImageError.o
+X86MAC64/mrcImageGet.o:mrcImageGet.o
+X86MAC64/mrcImageInfo.o:mrcImageInfo.o
+X86MAC64/mrcImageInit.o:mrcImageInit.o
+X86MAC64/mrcImageOperation.o:mrcImageOperation.o
+X86MAC64/mrcImagePVM.o:mrcImagePVM.o
+X86MAC64/mrcImagePrint.o:mrcImagePrint.o
+X86MAC64/mrcImageRead.o:mrcImageRead.o
+X86MAC64/mrcImageSectionGet.o:mrcImageSectionGet.o
+X86MAC64/mrcImageSectionSet.o:mrcImageSectionSet.o
+X86MAC64/mrcImageSet.o:mrcImageSet.o
+X86MAC64/mrcImageTailer.o:mrcImageTailer.o
+X86MAC64/mrcImageToIntImage.o:mrcImageToIntImage.o
+X86MAC64/mrcImageUtil.o:mrcImageUtil.o
+X86MAC64/mrcImageUtilityforVariance.o:mrcImageUtilityforVariance.o
+X86MAC64/mrcImageWrite.o:mrcImageWrite.o
+X86MAC64/mrcImageWrite2.o:mrcImageWrite2.o
+X86MAC64/mrcImagefuncmin.o:mrcImagefuncmin.o
+X86MAC64/mrcRefUtil.o:mrcRefUtil.o

diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/fftn.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/fftn.sharedo
index 40135f1..2137998 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a b/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a
index b7e058f..5ec6e20 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a b/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a
index db7f0a5..50d5f8e 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFETnormalizeBySD.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFETnormalizeBySD.sharedo
index 53c6de5..b1c36a1 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTExpression.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTExpression.sharedo
index beb622c..ba948ff 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTFGconj.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTFGconj.sharedo
index 2430078..9910c8c 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTFxG.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTFxG.sharedo
index f66176a..dd7672b 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTInfo.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcFFTInfo.sharedo
index a114323..548d04d 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImage3DWindowing.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImage3DWindowing.sharedo
index 04e78b9..f218f2d 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageAddValue.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageAddValue.sharedo
index 407c724..9ed424e 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageAsProbability.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageAsProbability.sharedo
index ee4a00c..45ab08f 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageAverage.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageAverage.sharedo
index d9899c5..315546a 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageBandPassFilter.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageBandPassFilter.sharedo
index 95a7d3e..2d093ea 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageBilateralFilter.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageBilateralFilter.sharedo
index 735fa64..f1c65e4 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageBinarization.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageBinarization.sharedo
index 8487a3d..157b788 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFCompensation.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFCompensation.sharedo
index d629607..c1691b0 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFDetermination.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFDetermination.sharedo
index f9634da..cab7661 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFObservation.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFObservation.sharedo
index d0460aa..a45f061 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFSN.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCTFSN.sharedo
index db414ba..634d7f4 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCVE.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCVE.sharedo
index 397d51e..6a0248d 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCalcArea.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCalcArea.sharedo
index 673bf9b..55f661a 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCenterGet.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCenterGet.sharedo
index 1352e6b..0bc3db2 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCentre.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCentre.sharedo
index e598c9f..6def68b 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageClosing.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageClosing.sharedo
index 7184e96..09339b4 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageClusterAnalysis.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageClusterAnalysis.sharedo
index 51fbbd5..94cce39 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCommonLine.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCommonLine.sharedo
index 45ca98c..ff22be1 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageConnection.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageConnection.sharedo
index 8bc1aa6..75cc771 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageConnectivityNumberCalc.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageConnectivityNumberCalc.sharedo
index 9ab3bd9..c677088 100644 (file)
Binary files a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageConnectivityNumberCalc.sharedo and b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageConnectivityNumberCalc.sharedo differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageContourSurface.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageContourSurface.sharedo
index 8fb2912..5ca52fc 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo
index 16c2254..e2efbd3 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationWithCTFCompensation.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationWithCTFCompensation.sharedo
index 62ea073..84d06c4 100644 (file)
Binary files a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationWithCTFCompensation.sharedo and b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationWithCTFCompensation.sharedo differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationinSpace.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationinSpace.sharedo
index 284a31c..4f6914e 100644 (file)
Binary files a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationinSpace.sharedo and b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelationinSpace.sharedo differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCrystalCreate.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCrystalCreate.sharedo
index c57af8c..ecf53a9 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDataMaxAndMinGetByImage.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDataMaxAndMinGetByImage.sharedo
index 63e11ca..919bce7 100644 (file)
Binary files a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDataMaxAndMinGetByImage.sharedo and b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDataMaxAndMinGetByImage.sharedo differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDataStraightCopy.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDataStraightCopy.sharedo
index 5d4b681..ce90f27 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDensity.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDensity.sharedo
index 362f63a..37cbede 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDensityInverse.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDensityInverse.sharedo
index 96491f9..ea46b93 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDensityNormalizationByImage.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDensityNormalizationByImage.sharedo
index d310bdb..cb76a03 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDilation.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDilation.sharedo
index 75fd887..c034314 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDistanceConversion.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageDistanceConversion.sharedo
index 42210d4..29fbf2e 100644 (file)
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diff --git a/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageEdge.sharedo b/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageEdge.sharedo
index 0d233fe..0c6b665 100644 (file)
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index 18eadc5..b35e7b1 100644 (file)
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diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/.Depend b/src/Objects/DataManip/pdbFile/src/X86MAC64/.Depend
index 12541bd..56d6742 100644 (file)
--- a/src/Objects/DataManip/pdbFile/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/pdbFile/src/X86MAC64/.Depend
@@ -1,371 +1,15 @@
-lpdb2mrc2d.o: lpdb2mrc2d.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/pdbFile.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h lpdb2mrcInfo.h
-lpdb2mrc3d.o: lpdb2mrc3d.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/pdbFile.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h lpdb2mrcInfo.h
-lpdbCoord.o: lpdbCoord.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
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-  /Applications/Eos.app/Eos/include/Matrix3D.h \
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-  /Applications/Eos.app/Eos/include/Array.h \
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-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
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-  /usr/include/AvailabilityInternal.h lpdbCoordInfo.h ../inc/pdbFile.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
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-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
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-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
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-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/String.h \
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-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h lpdbSelectedAtom.h \
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-  /usr/include/AvailabilityInternal.h pdbInfoGet.h ../inc/pdbFile.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
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-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h lpdbSurface.h \
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-  /Applications/Eos.app/Eos/include/lmrcImageContourSurface.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
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-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
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-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
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-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
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-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
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-  /usr/include/limits.h /usr/include/machine/limits.h \
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-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
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-  /usr/include/math.h ../inc/pdbFile.h \
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-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
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-  /Applications/Eos.app/Eos/include/Matrix3D.h
-pdbSecondaryStructure.o: pdbSecondaryStructure.c \
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-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
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-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
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-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
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-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
-pdbSet.o: pdbSet.c ../inc/pdbFile.h /usr/include/stdio.h \
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-  /Applications/Eos.app/Eos/include/Matrix3D.h \
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-pdbTrans.o: pdbTrans.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
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+X86MAC64/lpdb2mrc2d.o:lpdb2mrc2d.o
+X86MAC64/lpdb2mrc3d.o:lpdb2mrc3d.o
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+X86MAC64/lpdbSelectedAtom.o:lpdbSelectedAtom.o
+X86MAC64/lpdbSurface.o:lpdbSurface.o
+X86MAC64/pdbFileRead.o:pdbFileRead.o
+X86MAC64/pdbFileWrite.o:pdbFileWrite.o
+X86MAC64/pdbGet.o:pdbGet.o
+X86MAC64/pdbInfoGet.o:pdbInfoGet.o
+X86MAC64/pdbRotation.o:pdbRotation.o
+X86MAC64/pdbSecondaryStructure.o:pdbSecondaryStructure.o
+X86MAC64/pdbSet.o:pdbSet.o
+X86MAC64/pdbTrans.o:pdbTrans.o
+X86MAC64/pdbUtil.o:pdbUtil.o

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.a b/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.a
index 07f8799..bb891e8 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.a and b/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.a differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.debug.a b/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.debug.a
index 0228249..8957369 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.debug.a and b/src/Objects/DataManip/pdbFile/src/X86MAC64/libpdbFile.debug.a differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc2d.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc2d.sharedo
index b9c76ff..a134a9a 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc2d.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc2d.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc3d.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc3d.sharedo
index f1ca97f..9214981 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc3d.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdb2mrc3d.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoord.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoord.sharedo
index 6ab8f26..e76fa84 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoord.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoord.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoordInfo.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoordInfo.sharedo
index 36e67e8..107d201 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoordInfo.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbCoordInfo.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSelectedAtom.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSelectedAtom.sharedo
index c6c4373..b25078a 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSelectedAtom.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSelectedAtom.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSurface.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSurface.sharedo
index 883018f..d496cee 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSurface.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/lpdbSurface.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileRead.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileRead.sharedo
index ffb45b6..2f114cc 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileRead.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileRead.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileWrite.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileWrite.sharedo
index c48aaf7..7754a95 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileWrite.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbFileWrite.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbGet.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbGet.sharedo
index 9596ac1..c9ee8d9 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbGet.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbGet.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbInfoGet.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbInfoGet.sharedo
index 27d9ee9..e895388 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbInfoGet.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbInfoGet.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbRotation.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbRotation.sharedo
index 920cfd2..83d44b3 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbRotation.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbRotation.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSecondaryStructure.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSecondaryStructure.sharedo
index bfed6bc..edc9853 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSecondaryStructure.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSecondaryStructure.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSet.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSet.sharedo
index 9d1789c..a8ed567 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSet.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbSet.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbTrans.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbTrans.sharedo
index 5099194..38f93df 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbTrans.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbTrans.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbUtil.sharedo b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbUtil.sharedo
index 9b82113..f2227d7 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbUtil.sharedo and b/src/Objects/DataManip/pdbFile/src/X86MAC64/pdbUtil.sharedo differ

diff --git a/src/Objects/DataManip/simulation/src/X86MAC64/.Depend b/src/Objects/DataManip/simulation/src/X86MAC64/.Depend
index 31e02d1..f3f5b2f 100644 (file)
--- a/src/Objects/DataManip/simulation/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/simulation/src/X86MAC64/.Depend
@@ -1,33 +1 @@
-lFRET.o: lFRET.c /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/String.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h lFRET.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
+X86MAC64/lFRET.o:lFRET.o

diff --git a/src/Objects/DataManip/simulation/src/X86MAC64/lFRET.sharedo b/src/Objects/DataManip/simulation/src/X86MAC64/lFRET.sharedo
index a911588..bdc88d0 100644 (file)
Binary files a/src/Objects/DataManip/simulation/src/X86MAC64/lFRET.sharedo and b/src/Objects/DataManip/simulation/src/X86MAC64/lFRET.sharedo differ

diff --git a/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.a b/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.a
index afbfa19..0161f79 100644 (file)
Binary files a/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.a and b/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.a differ

diff --git a/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.debug.a b/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.debug.a
index ebf7910..b9631c8 100644 (file)
Binary files a/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.debug.a and b/src/Objects/DataManip/simulation/src/X86MAC64/libsimulation.debug.a differ

diff --git a/src/Objects/DataManip/tgaFile/src/X86MAC64/.Depend b/src/Objects/DataManip/tgaFile/src/X86MAC64/.Depend
index 85c255f..1f19897 100644 (file)
--- a/src/Objects/DataManip/tgaFile/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/tgaFile/src/X86MAC64/.Depend
@@ -1,58 +1,3 @@
-tgaFileInit.o: tgaFileInit.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/tgaFile.h
-tgaFilePrint.o: tgaFilePrint.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h ../inc/tgaFile.h
-tgaFileRead.o: tgaFileRead.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/tgaFile.h
+X86MAC64/tgaFileInit.o:tgaFileInit.o
+X86MAC64/tgaFilePrint.o:tgaFilePrint.o
+X86MAC64/tgaFileRead.o:tgaFileRead.o

diff --git a/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.a b/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.a
index 8819cdd..cca5f47 100644 (file)
Binary files a/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.a and b/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.a differ

diff --git a/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.debug.a b/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.debug.a
index ceac045..43c4bc3 100644 (file)
Binary files a/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.debug.a and b/src/Objects/DataManip/tgaFile/src/X86MAC64/libtgaFile.debug.a differ

diff --git a/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileInit.sharedo b/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileInit.sharedo
index f2fc426..7190be4 100644 (file)
Binary files a/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileInit.sharedo and b/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileInit.sharedo differ

diff --git a/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFilePrint.sharedo b/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFilePrint.sharedo
index d05d355..989c6be 100644 (file)
Binary files a/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFilePrint.sharedo and b/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFilePrint.sharedo differ

diff --git a/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileRead.sharedo b/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileRead.sharedo
index 47214e4..62d95a3 100644 (file)
Binary files a/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileRead.sharedo and b/src/Objects/DataManip/tgaFile/src/X86MAC64/tgaFileRead.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/.Depend b/src/Objects/DataManip/transform/src/X86MAC64/.Depend
index 547d964..e3386dc 100644 (file)
--- a/src/Objects/DataManip/transform/src/X86MAC64/.Depend
+++ b/src/Objects/DataManip/transform/src/X86MAC64/.Depend
@@ -1,1019 +1,31 @@
-lAllCommonLineCalculation.o: lAllCommonLineCalculation.c \
-  lmrcImageOrientationSearchBySimultaneousMinimization.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/genUtil.h lCommonLineCalculation.h \
-  /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
-lAngularWeightCalculation.o: lAngularWeightCalculation.c \
-  lmrcImageOrientationSearchBySimultaneousMinimization.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
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-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdlib.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
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-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lllExtract.h \
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-  /Applications/Eos.app/Eos/include/ctfInfo.h \
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-  /Applications/Eos.app/Eos/include/Matrix3D.h \
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-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h
-lllExtract.o: lllExtract.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
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-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
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-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h lllExtract.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/lllDataFit.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h
-lllExtractCtfinfFileCreate.o: lllExtractCtfinfFileCreate.c \
-  lllExtractCtfinfFileCreate.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/ctfZeroPoint.h
-lllExtractWithSeparation.o: lllExtractWithSeparation.c \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/nr2.h \
-  lllExtract.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/lllDataFit.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h \
-  /Applications/Eos.app/Eos/include/lllDataMergeDifferentN.h
-lllExtractdYEstimate.o: lllExtractdYEstimate.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h lllExtractdYEstimate.h
-lmrc2Dto3D.o: lmrc2Dto3D.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
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-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/eosPThread.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h \
-  lmrc2Dto3D.h /Applications/Eos.app/Eos/include/genUtil.h \
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-  /Applications/Eos.app/Eos/include/String.h \
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-  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h lmrc3Dto2D.h \
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-  /Applications/Eos.app/Eos/include/./lmrcImageRhoFiltering.h
-lmrc2Dto3DSIRT.o: lmrc2Dto3DSIRT.c \
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-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
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-  /usr/include/AvailabilityInternal.h lmrc3Dto2D.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
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-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h lmrc3Dto2D.h lmrc2Dto3D.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
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-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/lmrcImageRhoFiltering.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSubtractionCalc.h \
-  /Applications/Eos.app/Eos/include/lmrcImageDensityNormalizationByImage.h
-lmrc3Dto2D.o: lmrc3Dto2D.c /Applications/Eos.app/Eos/include/File.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h \
-  /Applications/Eos.app/Eos/include/eosPThread.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h \
-  lmrc3Dto2D.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h lmrc3Dto2D.h
-lmrcImageFileListAndEulerAngleDataRead.o:  \
- lmrcImageFileListAndEulerAngleDataRead.c \
-  lmrcImageFileListAndEulerAngleDataRead.h /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
-lmrcImageOneLineGet.o: lmrcImageOneLineGet.c \
-  lmrcImageOrientationSearchBySimultaneousMinimization.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/genUtil.h lCommonLineCalculation.h \
-  /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
-lmrcImageSinogramCorrelationAdditionalWeight.o:  \
- lmrcImageSinogramCorrelationAdditionalWeight.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/./lmrcImageSinogram.h \
-  /Applications/Eos.app/Eos/include/./mrcImage.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/./genUtil.h \
-  /Applications/Eos.app/Eos/include/./ctfInfo.h \
-  /Applications/Eos.app/Eos/include/./Vector.h \
-  /Applications/Eos.app/Eos/include/./Matrix3D.h \
-  /Applications/Eos.app/Eos/include/./Array.h \
-  /Applications/Eos.app/Eos/include/./lmrcImageBinarization.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
+X86MAC64/lAllCommonLineCalculation.o:lAllCommonLineCalculation.o
+X86MAC64/lAngularWeightCalculation.o:lAngularWeightCalculation.o
+X86MAC64/lCommonLineCalculation.o:lCommonLineCalculation.o
+X86MAC64/lCommonLineDataSetInPlaneRotation.o:lCommonLineDataSetInPlaneRotation.o
+X86MAC64/lCommonLinesDataSet.o:lCommonLinesDataSet.o
+X86MAC64/lDescartesIntoPolar.o:lDescartesIntoPolar.o
+X86MAC64/lEvaluateCorrelationMapwithCommonLine.o:lEvaluateCorrelationMapwithCommonLine.o
+X86MAC64/lFETOrientationSearchByAnnealing.o:lFETOrientationSearchByAnnealing.o
+X86MAC64/lFETOrientationSearchByFeatureAlignment.o:lFETOrientationSearchByFeatureAlignment.o
+X86MAC64/lFETOrientationSearchByFeatureAlignmentInitSet.o:lFETOrientationSearchByFeatureAlignmentInitSet.o
+X86MAC64/lFETOrientationSearchByFeatureAlignmentSphere.o:lFETOrientationSearchByFeatureAlignmentSphere.o
+X86MAC64/lFETmapOrientationSearchBySimultaneousFitting.o:lFETmapOrientationSearchBySimultaneousFitting.o
+X86MAC64/lFETsmallMapSetCreate_forSimultaneousMinimization.o:lFETsmallMapSetCreate_forSimultaneousMinimization.o
+X86MAC64/lInitialDataFileRead.o:lInitialDataFileRead.o
+X86MAC64/lJcalulation.o:lJcalulation.o
+X86MAC64/lLcalculation.o:lLcalculation.o
+X86MAC64/lPlaneRotationAngleSet.o:lPlaneRotationAngleSet.o
+X86MAC64/lllDataSeparationInfoPrint.o:lllDataSeparationInfoPrint.o
+X86MAC64/lllDataSeparationInfoRead.o:lllDataSeparationInfoRead.o
+X86MAC64/lllDataSeparationInfoSet.o:lllDataSeparationInfoSet.o
+X86MAC64/lllDatarMaxLimitForSeparation.o:lllDatarMaxLimitForSeparation.o
+X86MAC64/lllExtract.o:lllExtract.o
+X86MAC64/lllExtractCtfinfFileCreate.o:lllExtractCtfinfFileCreate.o
+X86MAC64/lllExtractWithSeparation.o:lllExtractWithSeparation.o
+X86MAC64/lllExtractdYEstimate.o:lllExtractdYEstimate.o
+X86MAC64/lmrc2Dto3D.o:lmrc2Dto3D.o
+X86MAC64/lmrc2Dto3DSIRT.o:lmrc2Dto3DSIRT.o
+X86MAC64/lmrc3Dto2D.o:lmrc3Dto2D.o
+X86MAC64/lmrcImageFileListAndEulerAngleDataRead.o:lmrcImageFileListAndEulerAngleDataRead.o
+X86MAC64/lmrcImageOneLineGet.o:lmrcImageOneLineGet.o
+X86MAC64/lmrcImageSinogramCorrelationAdditionalWeight.o:lmrcImageSinogramCorrelationAdditionalWeight.o

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lAllCommonLineCalculation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lAllCommonLineCalculation.sharedo
index 3bad59a..64bbcb2 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lAllCommonLineCalculation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lAllCommonLineCalculation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lAngularWeightCalculation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lAngularWeightCalculation.sharedo
index 753a43f..02d5bd9 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lAngularWeightCalculation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lAngularWeightCalculation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineCalculation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineCalculation.sharedo
index eb7700c..dd04d78 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineCalculation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineCalculation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineDataSetInPlaneRotation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineDataSetInPlaneRotation.sharedo
index 768cdb4..42bfe3a 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineDataSetInPlaneRotation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lCommonLineDataSetInPlaneRotation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lCommonLinesDataSet.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lCommonLinesDataSet.sharedo
index a78fb3f..e32fd76 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lCommonLinesDataSet.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lCommonLinesDataSet.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lDescartesIntoPolar.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lDescartesIntoPolar.sharedo
index f54b393..2255980 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lDescartesIntoPolar.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lDescartesIntoPolar.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lEvaluateCorrelationMapwithCommonLine.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lEvaluateCorrelationMapwithCommonLine.sharedo
index 676da19..877b2f4 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lEvaluateCorrelationMapwithCommonLine.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lEvaluateCorrelationMapwithCommonLine.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByAnnealing.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByAnnealing.sharedo
index 47ebf2a..fb3c1be 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByAnnealing.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByAnnealing.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignment.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignment.sharedo
index 5a8aae7..0ab65fa 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignment.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignment.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentInitSet.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentInitSet.sharedo
index 373aa13..31ff1e5 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentInitSet.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentInitSet.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentSphere.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentSphere.sharedo
index 11c3280..e4d34c1 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentSphere.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lFETOrientationSearchByFeatureAlignmentSphere.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lFETmapOrientationSearchBySimultaneousFitting.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lFETmapOrientationSearchBySimultaneousFitting.sharedo
index 6a08485..280b0d8 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lFETmapOrientationSearchBySimultaneousFitting.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lFETmapOrientationSearchBySimultaneousFitting.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lFETsmallMapSetCreate_forSimultaneousMinimization.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lFETsmallMapSetCreate_forSimultaneousMinimization.sharedo
index e47bfb3..0866ee8 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lFETsmallMapSetCreate_forSimultaneousMinimization.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lFETsmallMapSetCreate_forSimultaneousMinimization.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lInitialDataFileRead.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lInitialDataFileRead.sharedo
index 0419750..02d048d 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lInitialDataFileRead.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lInitialDataFileRead.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lJcalulation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lJcalulation.sharedo
index 0a27ed4..6212006 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lJcalulation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lJcalulation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lLcalculation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lLcalculation.sharedo
index e1b3967..53965d0 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lLcalculation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lLcalculation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lPlaneRotationAngleSet.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lPlaneRotationAngleSet.sharedo
index 7ed3f2b..52c3220 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lPlaneRotationAngleSet.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lPlaneRotationAngleSet.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/libtransform.a b/src/Objects/DataManip/transform/src/X86MAC64/libtransform.a
index e0f3833..4e2c789 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/libtransform.a and b/src/Objects/DataManip/transform/src/X86MAC64/libtransform.a differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/libtransform.debug.a b/src/Objects/DataManip/transform/src/X86MAC64/libtransform.debug.a
index 2a29de7..ff5c293 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/libtransform.debug.a and b/src/Objects/DataManip/transform/src/X86MAC64/libtransform.debug.a differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoRead.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoRead.sharedo
index 09d9498..b6a6ae5 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoRead.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoRead.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoSet.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoSet.sharedo
index 7b12e88..9573df3 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoSet.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lllDataSeparationInfoSet.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lllDatarMaxLimitForSeparation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lllDatarMaxLimitForSeparation.sharedo
index d5cc4a1..c05ba58 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lllDatarMaxLimitForSeparation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lllDatarMaxLimitForSeparation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lllExtract.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lllExtract.sharedo
index d1f5a0b..93a33e8 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lllExtract.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lllExtract.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lllExtractCtfinfFileCreate.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lllExtractCtfinfFileCreate.sharedo
index e83e54e..9283e5c 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lllExtractCtfinfFileCreate.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lllExtractCtfinfFileCreate.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lllExtractWithSeparation.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lllExtractWithSeparation.sharedo
index 377affb..af63651 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lllExtractWithSeparation.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lllExtractWithSeparation.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lllExtractdYEstimate.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lllExtractdYEstimate.sharedo
index d4cad9d..accb988 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lllExtractdYEstimate.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lllExtractdYEstimate.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3D.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3D.sharedo
index 72e72a4..8750517 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3D.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3D.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3DSIRT.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3DSIRT.sharedo
index 378490a..c9110cf 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3DSIRT.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lmrc2Dto3DSIRT.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lmrc3Dto2D.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lmrc3Dto2D.sharedo
index 0ac1438..712b47d 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lmrc3Dto2D.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lmrc3Dto2D.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageFileListAndEulerAngleDataRead.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageFileListAndEulerAngleDataRead.sharedo
index 8bff267..fefc8c1 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageFileListAndEulerAngleDataRead.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageFileListAndEulerAngleDataRead.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageOneLineGet.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageOneLineGet.sharedo
index cbf87c6..17c4c08 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageOneLineGet.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageOneLineGet.sharedo differ

diff --git a/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageSinogramCorrelationAdditionalWeight.sharedo b/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageSinogramCorrelationAdditionalWeight.sharedo
index 987bc92..a56fb69 100644 (file)
Binary files a/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageSinogramCorrelationAdditionalWeight.sharedo and b/src/Objects/DataManip/transform/src/X86MAC64/lmrcImageSinogramCorrelationAdditionalWeight.sharedo differ

diff --git a/src/Objects/General/AI/src/X86MAC64/.Depend b/src/Objects/General/AI/src/X86MAC64/.Depend
index aaf319e..3a052f0 100644 (file)
--- a/src/Objects/General/AI/src/X86MAC64/.Depend
+++ b/src/Objects/General/AI/src/X86MAC64/.Depend
@@ -1,58 +1,2 @@
-lmrcNeuralNet.o: lmrcNeuralNet.c \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h NeuralNet.h lmrcNeuralNet.h NeuralNet.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h
-neuralNet.o: neuralNet.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h NeuralNet.h /usr/include/time.h \
-  /usr/include/_structs.h
+X86MAC64/lmrcNeuralNet.o:lmrcNeuralNet.o
+X86MAC64/neuralNet.o:neuralNet.o

diff --git a/src/Objects/General/AI/src/X86MAC64/libAI.a b/src/Objects/General/AI/src/X86MAC64/libAI.a
index 7c490cc..6236ee2 100644 (file)
Binary files a/src/Objects/General/AI/src/X86MAC64/libAI.a and b/src/Objects/General/AI/src/X86MAC64/libAI.a differ

diff --git a/src/Objects/General/AI/src/X86MAC64/libAI.debug.a b/src/Objects/General/AI/src/X86MAC64/libAI.debug.a
index 9d4c2b4..6bc63fc 100644 (file)
Binary files a/src/Objects/General/AI/src/X86MAC64/libAI.debug.a and b/src/Objects/General/AI/src/X86MAC64/libAI.debug.a differ

diff --git a/src/Objects/General/AI/src/X86MAC64/lmrcNeuralNet.sharedo b/src/Objects/General/AI/src/X86MAC64/lmrcNeuralNet.sharedo
index cf1eda8..ce1e1e3 100644 (file)
Binary files a/src/Objects/General/AI/src/X86MAC64/lmrcNeuralNet.sharedo and b/src/Objects/General/AI/src/X86MAC64/lmrcNeuralNet.sharedo differ

diff --git a/src/Objects/General/AI/src/X86MAC64/neuralNet.sharedo b/src/Objects/General/AI/src/X86MAC64/neuralNet.sharedo
index d0f0f94..0d4d882 100644 (file)
Binary files a/src/Objects/General/AI/src/X86MAC64/neuralNet.sharedo and b/src/Objects/General/AI/src/X86MAC64/neuralNet.sharedo differ

diff --git a/src/Objects/General/Array/src/X86MAC64/.Depend b/src/Objects/General/Array/src/X86MAC64/.Depend
index 6117442..9f8d003 100644 (file)
--- a/src/Objects/General/Array/src/X86MAC64/.Depend
+++ b/src/Objects/General/Array/src/X86MAC64/.Depend
@@ -1,116 +1,6 @@
-arrayInfo.o: arrayInfo.c ../inc/Array.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h
-arrayInit.o: arrayInit.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-arrayPCA.o: arrayPCA.c ../inc/Array.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /Applications/Eos.app/Eos/include/nr2.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h
-arrayRead.o: arrayRead.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
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-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h
-arrayWrite.o: arrayWrite.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
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-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Array.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h
-larray2mrc.o: larray2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/Array.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h larray2mrc.h
+X86MAC64/arrayInfo.o:arrayInfo.o
+X86MAC64/arrayInit.o:arrayInit.o
+X86MAC64/arrayPCA.o:arrayPCA.o
+X86MAC64/arrayRead.o:arrayRead.o
+X86MAC64/arrayWrite.o:arrayWrite.o
+X86MAC64/larray2mrc.o:larray2mrc.o

diff --git a/src/Objects/General/Array/src/X86MAC64/arrayInfo.sharedo b/src/Objects/General/Array/src/X86MAC64/arrayInfo.sharedo
index cd7795a..b8489a1 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/arrayInfo.sharedo and b/src/Objects/General/Array/src/X86MAC64/arrayInfo.sharedo differ

diff --git a/src/Objects/General/Array/src/X86MAC64/arrayInit.sharedo b/src/Objects/General/Array/src/X86MAC64/arrayInit.sharedo
index 931a06a..9512f4b 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/arrayInit.sharedo and b/src/Objects/General/Array/src/X86MAC64/arrayInit.sharedo differ

diff --git a/src/Objects/General/Array/src/X86MAC64/arrayPCA.sharedo b/src/Objects/General/Array/src/X86MAC64/arrayPCA.sharedo
index b1f2d0a..747e9d6 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/arrayPCA.sharedo and b/src/Objects/General/Array/src/X86MAC64/arrayPCA.sharedo differ

diff --git a/src/Objects/General/Array/src/X86MAC64/arrayRead.sharedo b/src/Objects/General/Array/src/X86MAC64/arrayRead.sharedo
index 0e7f994..64f316b 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/arrayRead.sharedo and b/src/Objects/General/Array/src/X86MAC64/arrayRead.sharedo differ

diff --git a/src/Objects/General/Array/src/X86MAC64/arrayWrite.sharedo b/src/Objects/General/Array/src/X86MAC64/arrayWrite.sharedo
index e309140..aa5488e 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/arrayWrite.sharedo and b/src/Objects/General/Array/src/X86MAC64/arrayWrite.sharedo differ

diff --git a/src/Objects/General/Array/src/X86MAC64/larray2mrc.sharedo b/src/Objects/General/Array/src/X86MAC64/larray2mrc.sharedo
index f84af7d..8af1f6f 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/larray2mrc.sharedo and b/src/Objects/General/Array/src/X86MAC64/larray2mrc.sharedo differ

diff --git a/src/Objects/General/Array/src/X86MAC64/libArray.a b/src/Objects/General/Array/src/X86MAC64/libArray.a
index 896ecd7..e7377ce 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/libArray.a and b/src/Objects/General/Array/src/X86MAC64/libArray.a differ

diff --git a/src/Objects/General/Array/src/X86MAC64/libArray.debug.a b/src/Objects/General/Array/src/X86MAC64/libArray.debug.a
index 793b4e8..65a7a9c 100644 (file)
Binary files a/src/Objects/General/Array/src/X86MAC64/libArray.debug.a and b/src/Objects/General/Array/src/X86MAC64/libArray.debug.a differ

diff --git a/src/Objects/General/Cluster/src/X86MAC64/.Depend b/src/Objects/General/Cluster/src/X86MAC64/.Depend
index f806321..355da2c 100644 (file)
--- a/src/Objects/General/Cluster/src/X86MAC64/.Depend
+++ b/src/Objects/General/Cluster/src/X86MAC64/.Depend
@@ -1,115 +1,5 @@
-clusterLogAnalysis.o: clusterLogAnalysis.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/Vector.h \
-  ../inc/Cluster.h
-clusterLogInit.o: clusterLogInit.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
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-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
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-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Cluster.h
-clusterLogUtil.o: clusterLogUtil.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
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-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
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-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/String.h \
-  ../inc/Cluster.h
-clusterLogWrite.o: clusterLogWrite.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/Cluster.h \
-  /Applications/Eos.app/Eos/include/psFile.h \
-  /Applications/Eos.app/Eos/include/File.h
+X86MAC64/clusterLogAnalysis.o:clusterLogAnalysis.o
+X86MAC64/clusterLogInit.o:clusterLogInit.o
+X86MAC64/clusterLogRead.o:clusterLogRead.o
+X86MAC64/clusterLogUtil.o:clusterLogUtil.o
+X86MAC64/clusterLogWrite.o:clusterLogWrite.o

diff --git a/src/Objects/General/Cluster/src/X86MAC64/clusterLogAnalysis.sharedo b/src/Objects/General/Cluster/src/X86MAC64/clusterLogAnalysis.sharedo
index 40c49d0..c759e7b 100644 (file)
Binary files a/src/Objects/General/Cluster/src/X86MAC64/clusterLogAnalysis.sharedo and b/src/Objects/General/Cluster/src/X86MAC64/clusterLogAnalysis.sharedo differ

diff --git a/src/Objects/General/Cluster/src/X86MAC64/clusterLogInit.sharedo b/src/Objects/General/Cluster/src/X86MAC64/clusterLogInit.sharedo
index 9618e55..74d8b3b 100644 (file)
Binary files a/src/Objects/General/Cluster/src/X86MAC64/clusterLogInit.sharedo and b/src/Objects/General/Cluster/src/X86MAC64/clusterLogInit.sharedo differ

diff --git a/src/Objects/General/Cluster/src/X86MAC64/clusterLogUtil.sharedo b/src/Objects/General/Cluster/src/X86MAC64/clusterLogUtil.sharedo
index 8d7a7c4..d999292 100644 (file)
Binary files a/src/Objects/General/Cluster/src/X86MAC64/clusterLogUtil.sharedo and b/src/Objects/General/Cluster/src/X86MAC64/clusterLogUtil.sharedo differ

diff --git a/src/Objects/General/Cluster/src/X86MAC64/clusterLogWrite.sharedo b/src/Objects/General/Cluster/src/X86MAC64/clusterLogWrite.sharedo
index 9057c48..408370e 100644 (file)
Binary files a/src/Objects/General/Cluster/src/X86MAC64/clusterLogWrite.sharedo and b/src/Objects/General/Cluster/src/X86MAC64/clusterLogWrite.sharedo differ

diff --git a/src/Objects/General/Cluster/src/X86MAC64/libCluster.a b/src/Objects/General/Cluster/src/X86MAC64/libCluster.a
index e8c5601..2593e0a 100644 (file)
Binary files a/src/Objects/General/Cluster/src/X86MAC64/libCluster.a and b/src/Objects/General/Cluster/src/X86MAC64/libCluster.a differ

diff --git a/src/Objects/General/Cluster/src/X86MAC64/libCluster.debug.a b/src/Objects/General/Cluster/src/X86MAC64/libCluster.debug.a
index afafbfb..5e0c916 100644 (file)
Binary files a/src/Objects/General/Cluster/src/X86MAC64/libCluster.debug.a and b/src/Objects/General/Cluster/src/X86MAC64/libCluster.debug.a differ

diff --git a/src/Objects/General/Crystal/src/X86MAC64/.Depend b/src/Objects/General/Crystal/src/X86MAC64/.Depend
index f88df7a..eef5b62 100644 (file)
--- a/src/Objects/General/Crystal/src/X86MAC64/.Depend
+++ b/src/Objects/General/Crystal/src/X86MAC64/.Depend
@@ -1,61 +1,4 @@
-crystalHelix.o: crystalHelix.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/Crystal.h
-crystalInfoFile.o: crystalInfoFile.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/String.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h ../inc/Crystal.h
-crystalInit.o: crystalInit.c ../inc/Crystal.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h
-crystalUtil.o: crystalUtil.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/Crystal.h
+X86MAC64/crystalHelix.o:crystalHelix.o
+X86MAC64/crystalInfoFile.o:crystalInfoFile.o
+X86MAC64/crystalInit.o:crystalInit.o
+X86MAC64/crystalUtil.o:crystalUtil.o

diff --git a/src/Objects/General/Crystal/src/X86MAC64/crystalHelix.sharedo b/src/Objects/General/Crystal/src/X86MAC64/crystalHelix.sharedo
index 4184592..a3fff0b 100644 (file)
Binary files a/src/Objects/General/Crystal/src/X86MAC64/crystalHelix.sharedo and b/src/Objects/General/Crystal/src/X86MAC64/crystalHelix.sharedo differ

diff --git a/src/Objects/General/Crystal/src/X86MAC64/crystalInfoFile.sharedo b/src/Objects/General/Crystal/src/X86MAC64/crystalInfoFile.sharedo
index e29ce51..c0528f6 100644 (file)
Binary files a/src/Objects/General/Crystal/src/X86MAC64/crystalInfoFile.sharedo and b/src/Objects/General/Crystal/src/X86MAC64/crystalInfoFile.sharedo differ

diff --git a/src/Objects/General/Crystal/src/X86MAC64/crystalInit.sharedo b/src/Objects/General/Crystal/src/X86MAC64/crystalInit.sharedo
index 96a5943..4181165 100644 (file)
Binary files a/src/Objects/General/Crystal/src/X86MAC64/crystalInit.sharedo and b/src/Objects/General/Crystal/src/X86MAC64/crystalInit.sharedo differ

diff --git a/src/Objects/General/Crystal/src/X86MAC64/crystalUtil.sharedo b/src/Objects/General/Crystal/src/X86MAC64/crystalUtil.sharedo
index ca7639f..3b88443 100644 (file)
Binary files a/src/Objects/General/Crystal/src/X86MAC64/crystalUtil.sharedo and b/src/Objects/General/Crystal/src/X86MAC64/crystalUtil.sharedo differ

diff --git a/src/Objects/General/Crystal/src/X86MAC64/libCrystal.a b/src/Objects/General/Crystal/src/X86MAC64/libCrystal.a
index 6834b33..a3bfc87 100644 (file)
Binary files a/src/Objects/General/Crystal/src/X86MAC64/libCrystal.a and b/src/Objects/General/Crystal/src/X86MAC64/libCrystal.a differ

diff --git a/src/Objects/General/Crystal/src/X86MAC64/libCrystal.debug.a b/src/Objects/General/Crystal/src/X86MAC64/libCrystal.debug.a
index 5d016d8..1c2edf6 100644 (file)
Binary files a/src/Objects/General/Crystal/src/X86MAC64/libCrystal.debug.a and b/src/Objects/General/Crystal/src/X86MAC64/libCrystal.debug.a differ

diff --git a/src/Objects/General/DataBase/src/X86MAC64/.Depend b/src/Objects/General/DataBase/src/X86MAC64/.Depend
index e69de29..12072c3 100644 (file)
--- a/src/Objects/General/DataBase/src/X86MAC64/.Depend
+++ b/src/Objects/General/DataBase/src/X86MAC64/.Depend
@@ -0,0 +1,10 @@
+X86MAC64/DataBase.o:DataBase.o
+X86MAC64/DataBase.o:DataBase.o
+X86MAC64/DataBaseCorba.o:DataBaseCorba.o
+X86MAC64/DataBaseCorba.o:DataBaseCorba.o
+X86MAC64/DataBaseCorbaBank.o:DataBaseCorbaBank.o
+X86MAC64/DataBaseCorbaImpl.o:DataBaseCorbaImpl.o
+X86MAC64/DataBaseCorbaManager.o:DataBaseCorbaManager.o
+X86MAC64/DataBaseJournal.o:DataBaseJournal.o
+X86MAC64/DataBaseMaker.o:DataBaseMaker.o
+X86MAC64/DataBaseNote.o:DataBaseNote.o

diff --git a/src/Objects/General/File/src/X86MAC64/.Depend b/src/Objects/General/File/src/X86MAC64/.Depend
index 49cfa28..c4d8540 100644 (file)
--- a/src/Objects/General/File/src/X86MAC64/.Depend
+++ b/src/Objects/General/File/src/X86MAC64/.Depend
@@ -1,55 +1,3 @@
-fileInfo.o: fileInfo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/File.h \
-  /Applications/Eos.app/Eos/include/String.h
-fileInit.o: fileInit.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/File.h
-fileOpen.o: fileOpen.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/File.h
+X86MAC64/fileInfo.o:fileInfo.o
+X86MAC64/fileInit.o:fileInit.o
+X86MAC64/fileOpen.o:fileOpen.o

diff --git a/src/Objects/General/File/src/X86MAC64/fileInfo.sharedo b/src/Objects/General/File/src/X86MAC64/fileInfo.sharedo
index ce3cfe2..6df9a49 100644 (file)
Binary files a/src/Objects/General/File/src/X86MAC64/fileInfo.sharedo and b/src/Objects/General/File/src/X86MAC64/fileInfo.sharedo differ

diff --git a/src/Objects/General/File/src/X86MAC64/fileInit.sharedo b/src/Objects/General/File/src/X86MAC64/fileInit.sharedo
index 0d566f4..a080792 100644 (file)
Binary files a/src/Objects/General/File/src/X86MAC64/fileInit.sharedo and b/src/Objects/General/File/src/X86MAC64/fileInit.sharedo differ

diff --git a/src/Objects/General/File/src/X86MAC64/fileOpen.sharedo b/src/Objects/General/File/src/X86MAC64/fileOpen.sharedo
index b0e9024..6d22772 100644 (file)
Binary files a/src/Objects/General/File/src/X86MAC64/fileOpen.sharedo and b/src/Objects/General/File/src/X86MAC64/fileOpen.sharedo differ

diff --git a/src/Objects/General/File/src/X86MAC64/libFile.a b/src/Objects/General/File/src/X86MAC64/libFile.a
index 2b73be7..0480613 100644 (file)
Binary files a/src/Objects/General/File/src/X86MAC64/libFile.a and b/src/Objects/General/File/src/X86MAC64/libFile.a differ

diff --git a/src/Objects/General/File/src/X86MAC64/libFile.debug.a b/src/Objects/General/File/src/X86MAC64/libFile.debug.a
index 5c7f0b1..f682095 100644 (file)
Binary files a/src/Objects/General/File/src/X86MAC64/libFile.debug.a and b/src/Objects/General/File/src/X86MAC64/libFile.debug.a differ

diff --git a/src/Objects/General/Map2D/src/X86MAC64/.Depend b/src/Objects/General/Map2D/src/X86MAC64/.Depend
index c532c4c..10b9852 100644 (file)
--- a/src/Objects/General/Map2D/src/X86MAC64/.Depend
+++ b/src/Objects/General/Map2D/src/X86MAC64/.Depend
@@ -1,17 +1 @@
-map2DCoordGet.o: map2DCoordGet.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/Map2D.h
+X86MAC64/map2DCoordGet.o:map2DCoordGet.o

diff --git a/src/Objects/General/Map2D/src/X86MAC64/libMap2D.a b/src/Objects/General/Map2D/src/X86MAC64/libMap2D.a
index cb41a62..bdabf87 100644 (file)
Binary files a/src/Objects/General/Map2D/src/X86MAC64/libMap2D.a and b/src/Objects/General/Map2D/src/X86MAC64/libMap2D.a differ

diff --git a/src/Objects/General/Map2D/src/X86MAC64/libMap2D.debug.a b/src/Objects/General/Map2D/src/X86MAC64/libMap2D.debug.a
index 157ec86..12f34fc 100644 (file)
Binary files a/src/Objects/General/Map2D/src/X86MAC64/libMap2D.debug.a and b/src/Objects/General/Map2D/src/X86MAC64/libMap2D.debug.a differ

diff --git a/src/Objects/General/Map2D/src/X86MAC64/libMap2D.so b/src/Objects/General/Map2D/src/X86MAC64/libMap2D.so
index fbb3f22..da9af81 100755 (executable)
Binary files a/src/Objects/General/Map2D/src/X86MAC64/libMap2D.so and b/src/Objects/General/Map2D/src/X86MAC64/libMap2D.so differ

diff --git a/src/Objects/General/Map2D/src/X86MAC64/map2DCoordGet.sharedo b/src/Objects/General/Map2D/src/X86MAC64/map2DCoordGet.sharedo
index 5e7c08d..edf0b40 100644 (file)
Binary files a/src/Objects/General/Map2D/src/X86MAC64/map2DCoordGet.sharedo and b/src/Objects/General/Map2D/src/X86MAC64/map2DCoordGet.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/.Depend b/src/Objects/General/Matrix3D/src/X86MAC64/.Depend
index 03ab98d..38ba289 100644 (file)
--- a/src/Objects/General/Matrix3D/src/X86MAC64/.Depend
+++ b/src/Objects/General/Matrix3D/src/X86MAC64/.Depend
@@ -1,143 +1,11 @@
-matrix3DEulerAngleGet.o: matrix3DEulerAngleGet.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/genUtil.h ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-matrix3DEulerAngleSet.o: matrix3DEulerAngleSet.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h
-matrix3DEulerAngles.o: matrix3DEulerAngles.c /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/float.h \
-  ../inc/Matrix3D.h /Applications/Eos.app/Eos/include/Vector.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/include/Array.h
-matrix3DFile.o: matrix3DFile.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/String.h
-matrix3DInit.o: matrix3DInit.c ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /Applications/Eos.app/Eos/include/Array.h
-matrix3DMultiply.o: matrix3DMultiply.c ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /Applications/Eos.app/Eos/include/Array.h
-matrix3DMultiplyVector.o: matrix3DMultiplyVector.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/Vector.h \
-  ../inc/Matrix3D.h /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h
-matrix3DRotation.o: matrix3DRotation.c ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /Applications/Eos.app/Eos/include/Array.h \
-  /usr/include/math.h
-matrix3DTranslation.o: matrix3DTranslation.c ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /Applications/Eos.app/Eos/include/Array.h
-matrix3DUtil.o: matrix3DUtil.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Array.h
+X86MAC64/matrix3DEulerAngleGet.o:matrix3DEulerAngleGet.o
+X86MAC64/matrix3DEulerAngleSet.o:matrix3DEulerAngleSet.o
+X86MAC64/matrix3DEulerAngles.o:matrix3DEulerAngles.o
+X86MAC64/matrix3DFile.o:matrix3DFile.o
+X86MAC64/matrix3DInit.o:matrix3DInit.o
+X86MAC64/matrix3DMultiply.o:matrix3DMultiply.o
+X86MAC64/matrix3DMultiplyMatrix.o:matrix3DMultiplyMatrix.o
+X86MAC64/matrix3DMultiplyVector.o:matrix3DMultiplyVector.o
+X86MAC64/matrix3DRotation.o:matrix3DRotation.o
+X86MAC64/matrix3DTranslation.o:matrix3DTranslation.o
+X86MAC64/matrix3DUtil.o:matrix3DUtil.o

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/.Source b/src/Objects/General/Matrix3D/src/X86MAC64/.Source
index c2b83c2..ff88219 100644 (file)
--- a/src/Objects/General/Matrix3D/src/X86MAC64/.Source
+++ b/src/Objects/General/Matrix3D/src/X86MAC64/.Source
@@ -5,6 +5,7 @@ matrix3DEulerAngles.c \
 matrix3DFile.c \
 matrix3DInit.c \
 matrix3DMultiply.c \
+matrix3DMultiplyMatrix.c \
 matrix3DMultiplyVector.c \
 matrix3DRotation.c \
 matrix3DTranslation.c \
@@ -17,6 +18,7 @@ matrix3DEulerAngles.o \
 matrix3DFile.o \
 matrix3DInit.o \
 matrix3DMultiply.o \
+matrix3DMultiplyMatrix.o \
 matrix3DMultiplyVector.o \
 matrix3DRotation.o \
 matrix3DTranslation.o \
@@ -29,6 +31,7 @@ matrix3DEulerAngles.sharedo \
 matrix3DFile.sharedo \
 matrix3DInit.sharedo \
 matrix3DMultiply.sharedo \
+matrix3DMultiplyMatrix.sharedo \
 matrix3DMultiplyVector.sharedo \
 matrix3DRotation.sharedo \
 matrix3DTranslation.sharedo \
@@ -41,6 +44,7 @@ X86MAC64/matrix3DEulerAngles.o \
 X86MAC64/matrix3DFile.o \
 X86MAC64/matrix3DInit.o \
 X86MAC64/matrix3DMultiply.o \
+X86MAC64/matrix3DMultiplyMatrix.o \
 X86MAC64/matrix3DMultiplyVector.o \
 X86MAC64/matrix3DRotation.o \
 X86MAC64/matrix3DTranslation.o \
@@ -53,6 +57,7 @@ X86MAC64/matrix3DEulerAngles.sharedo \
 X86MAC64/matrix3DFile.sharedo \
 X86MAC64/matrix3DInit.sharedo \
 X86MAC64/matrix3DMultiply.sharedo \
+X86MAC64/matrix3DMultiplyMatrix.sharedo \
 X86MAC64/matrix3DMultiplyVector.sharedo \
 X86MAC64/matrix3DRotation.sharedo \
 X86MAC64/matrix3DTranslation.sharedo \
@@ -65,6 +70,7 @@ matrix3DEulerAngles.debugo \
 matrix3DFile.debugo \
 matrix3DInit.debugo \
 matrix3DMultiply.debugo \
+matrix3DMultiplyMatrix.debugo \
 matrix3DMultiplyVector.debugo \
 matrix3DRotation.debugo \
 matrix3DTranslation.debugo \
@@ -77,6 +83,7 @@ X86MAC64/matrix3DEulerAngles.debugo \
 X86MAC64/matrix3DFile.debugo \
 X86MAC64/matrix3DInit.debugo \
 X86MAC64/matrix3DMultiply.debugo \
+X86MAC64/matrix3DMultiplyMatrix.debugo \
 X86MAC64/matrix3DMultiplyVector.debugo \
 X86MAC64/matrix3DRotation.debugo \
 X86MAC64/matrix3DTranslation.debugo \
@@ -89,6 +96,7 @@ matrix3DEulerAngles.cudagdb.o \
 matrix3DFile.cudagdb.o \
 matrix3DInit.cudagdb.o \
 matrix3DMultiply.cudagdb.o \
+matrix3DMultiplyMatrix.cudagdb.o \
 matrix3DMultiplyVector.cudagdb.o \
 matrix3DRotation.cudagdb.o \
 matrix3DTranslation.cudagdb.o \
@@ -101,6 +109,7 @@ X86MAC64/matrix3DEulerAngles.cudagdb.o \
 X86MAC64/matrix3DFile.cudagdb.o \
 X86MAC64/matrix3DInit.cudagdb.o \
 X86MAC64/matrix3DMultiply.cudagdb.o \
+X86MAC64/matrix3DMultiplyMatrix.cudagdb.o \
 X86MAC64/matrix3DMultiplyVector.cudagdb.o \
 X86MAC64/matrix3DRotation.cudagdb.o \
 X86MAC64/matrix3DTranslation.cudagdb.o \

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.a b/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.a
index 908b068..2377fe5 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.a and b/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.a differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.debug.a b/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.debug.a
index 05c1d85..78fca54 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.debug.a and b/src/Objects/General/Matrix3D/src/X86MAC64/libMatrix3D.debug.a differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleGet.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleGet.sharedo
index 95edbf2..cc98512 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleGet.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleGet.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleSet.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleSet.sharedo
index c8f63bd..845928d 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleSet.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngleSet.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngles.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngles.sharedo
index e4cd2c6..bd64e78 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngles.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DEulerAngles.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DFile.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DFile.sharedo
index 3c35a9a..8e86aa8 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DFile.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DFile.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DInit.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DInit.sharedo
index 2b48ae9..d49c1a0 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DInit.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DInit.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiply.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiply.sharedo
index e6b2ebd..90146b9 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiply.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiply.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiplyMatrix.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiplyMatrix.sharedo
new file mode 100644 (file)
index 0000000..13ee1e9
Binary files /dev/null and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiplyMatrix.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiplyVector.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiplyVector.sharedo
index bcfca39..c1154c6 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiplyVector.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DMultiplyVector.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DRotation.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DRotation.sharedo
index 0cba20c..98b4580 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DRotation.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DRotation.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DTranslation.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DTranslation.sharedo
index c5750ce..0e4c0ac 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DTranslation.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DTranslation.sharedo differ

diff --git a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DUtil.sharedo b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DUtil.sharedo
index 8ff2cac..9bd882d 100644 (file)
Binary files a/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DUtil.sharedo and b/src/Objects/General/Matrix3D/src/X86MAC64/matrix3DUtil.sharedo differ

diff --git a/src/Objects/General/Memory/src/X86MAC64/.Depend b/src/Objects/General/Memory/src/X86MAC64/.Depend
index c5f22aa..00aa442 100644 (file)
--- a/src/Objects/General/Memory/src/X86MAC64/.Depend
+++ b/src/Objects/General/Memory/src/X86MAC64/.Depend
@@ -1,98 +1,4 @@
-memoryAllocate.o: memoryAllocate.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-memoryByteSwap.o: memoryByteSwap.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/stdio.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  ../inc/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-memoryClear.o: memoryClear.c ../inc/Memory.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h
-memoryCopy.o: memoryCopy.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
+X86MAC64/memoryAllocate.o:memoryAllocate.o
+X86MAC64/memoryByteSwap.o:memoryByteSwap.o
+X86MAC64/memoryClear.o:memoryClear.o
+X86MAC64/memoryCopy.o:memoryCopy.o

diff --git a/src/Objects/General/Memory/src/X86MAC64/libMemory.a b/src/Objects/General/Memory/src/X86MAC64/libMemory.a
index 376848c..bfac821 100644 (file)
Binary files a/src/Objects/General/Memory/src/X86MAC64/libMemory.a and b/src/Objects/General/Memory/src/X86MAC64/libMemory.a differ

diff --git a/src/Objects/General/Memory/src/X86MAC64/libMemory.debug.a b/src/Objects/General/Memory/src/X86MAC64/libMemory.debug.a
index 607b2f7..2a1fad8 100644 (file)
Binary files a/src/Objects/General/Memory/src/X86MAC64/libMemory.debug.a and b/src/Objects/General/Memory/src/X86MAC64/libMemory.debug.a differ

diff --git a/src/Objects/General/Memory/src/X86MAC64/libMemory.so b/src/Objects/General/Memory/src/X86MAC64/libMemory.so
index 66efd58..0ebb081 100755 (executable)
Binary files a/src/Objects/General/Memory/src/X86MAC64/libMemory.so and b/src/Objects/General/Memory/src/X86MAC64/libMemory.so differ

diff --git a/src/Objects/General/Memory/src/X86MAC64/memoryAllocate.sharedo b/src/Objects/General/Memory/src/X86MAC64/memoryAllocate.sharedo
index 5480739..2be5fa6 100644 (file)
Binary files a/src/Objects/General/Memory/src/X86MAC64/memoryAllocate.sharedo and b/src/Objects/General/Memory/src/X86MAC64/memoryAllocate.sharedo differ

diff --git a/src/Objects/General/Memory/src/X86MAC64/memoryByteSwap.sharedo b/src/Objects/General/Memory/src/X86MAC64/memoryByteSwap.sharedo
index 323152f..1565cd7 100644 (file)
Binary files a/src/Objects/General/Memory/src/X86MAC64/memoryByteSwap.sharedo and b/src/Objects/General/Memory/src/X86MAC64/memoryByteSwap.sharedo differ

diff --git a/src/Objects/General/Memory/src/X86MAC64/memoryClear.sharedo b/src/Objects/General/Memory/src/X86MAC64/memoryClear.sharedo
index dfba158..875d264 100644 (file)
Binary files a/src/Objects/General/Memory/src/X86MAC64/memoryClear.sharedo and b/src/Objects/General/Memory/src/X86MAC64/memoryClear.sharedo differ

diff --git a/src/Objects/General/Memory/src/X86MAC64/memoryCopy.sharedo b/src/Objects/General/Memory/src/X86MAC64/memoryCopy.sharedo
index ffc0419..28e2ec0 100644 (file)
Binary files a/src/Objects/General/Memory/src/X86MAC64/memoryCopy.sharedo and b/src/Objects/General/Memory/src/X86MAC64/memoryCopy.sharedo differ

diff --git a/src/Objects/General/PVM/src/X86MAC64/.Depend b/src/Objects/General/PVM/src/X86MAC64/.Depend
index bfb3ed2..c4fb32c 100644 (file)
--- a/src/Objects/General/PVM/src/X86MAC64/.Depend
+++ b/src/Objects/General/PVM/src/X86MAC64/.Depend
@@ -1 +1 @@
-pvmStart.o: pvmStart.c
+X86MAC64/pvmStart.o:pvmStart.o

diff --git a/src/Objects/General/PVM/src/X86MAC64/libPVM.a b/src/Objects/General/PVM/src/X86MAC64/libPVM.a
index ca5b532..5bf57d9 100644 (file)
Binary files a/src/Objects/General/PVM/src/X86MAC64/libPVM.a and b/src/Objects/General/PVM/src/X86MAC64/libPVM.a differ

diff --git a/src/Objects/General/PVM/src/X86MAC64/libPVM.debug.a b/src/Objects/General/PVM/src/X86MAC64/libPVM.debug.a
index a328c42..8fd4cde 100644 (file)
Binary files a/src/Objects/General/PVM/src/X86MAC64/libPVM.debug.a and b/src/Objects/General/PVM/src/X86MAC64/libPVM.debug.a differ

diff --git a/src/Objects/General/PVM/src/X86MAC64/libPVM.so b/src/Objects/General/PVM/src/X86MAC64/libPVM.so
index 170a59e..a54e32e 100755 (executable)
Binary files a/src/Objects/General/PVM/src/X86MAC64/libPVM.so and b/src/Objects/General/PVM/src/X86MAC64/libPVM.so differ

diff --git a/src/Objects/General/Random/src/X86MAC64/.Depend b/src/Objects/General/Random/src/X86MAC64/.Depend
index 52b5af9..f8fcb33 100644 (file)
--- a/src/Objects/General/Random/src/X86MAC64/.Depend
+++ b/src/Objects/General/Random/src/X86MAC64/.Depend
@@ -1,54 +1,3 @@
-randomNormal.o: randomNormal.c ../inc/Random.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h /usr/include/time.h \
-  /usr/include/_structs.h
-randomUniform.o: randomUniform.c ../inc/Random.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h /usr/include/time.h \
-  /usr/include/_structs.h
-srandom.o: srandom.c /usr/include/time.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/sys/timeb.h \
-  /usr/include/sys/appleapiopts.h ../inc/Random.h /usr/include/stdio.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h
+X86MAC64/randomNormal.o:randomNormal.o
+X86MAC64/randomUniform.o:randomUniform.o
+X86MAC64/srandom.o:srandom.o

diff --git a/src/Objects/General/Random/src/X86MAC64/libRandom.a b/src/Objects/General/Random/src/X86MAC64/libRandom.a
index 902f45c..92144ab 100644 (file)
Binary files a/src/Objects/General/Random/src/X86MAC64/libRandom.a and b/src/Objects/General/Random/src/X86MAC64/libRandom.a differ

diff --git a/src/Objects/General/Random/src/X86MAC64/libRandom.debug.a b/src/Objects/General/Random/src/X86MAC64/libRandom.debug.a
index caade7a..7d655d2 100644 (file)
Binary files a/src/Objects/General/Random/src/X86MAC64/libRandom.debug.a and b/src/Objects/General/Random/src/X86MAC64/libRandom.debug.a differ

diff --git a/src/Objects/General/Random/src/X86MAC64/libRandom.so b/src/Objects/General/Random/src/X86MAC64/libRandom.so
index 3d93857..4ef999d 100755 (executable)
Binary files a/src/Objects/General/Random/src/X86MAC64/libRandom.so and b/src/Objects/General/Random/src/X86MAC64/libRandom.so differ

diff --git a/src/Objects/General/Random/src/X86MAC64/randomNormal.sharedo b/src/Objects/General/Random/src/X86MAC64/randomNormal.sharedo
index 8850f27..fa3823e 100644 (file)
Binary files a/src/Objects/General/Random/src/X86MAC64/randomNormal.sharedo and b/src/Objects/General/Random/src/X86MAC64/randomNormal.sharedo differ

diff --git a/src/Objects/General/Random/src/X86MAC64/randomUniform.sharedo b/src/Objects/General/Random/src/X86MAC64/randomUniform.sharedo
index 995da68..9292875 100644 (file)
Binary files a/src/Objects/General/Random/src/X86MAC64/randomUniform.sharedo and b/src/Objects/General/Random/src/X86MAC64/randomUniform.sharedo differ

diff --git a/src/Objects/General/Random/src/X86MAC64/srandom.sharedo b/src/Objects/General/Random/src/X86MAC64/srandom.sharedo
index 11ca2c0..667d77f 100644 (file)
Binary files a/src/Objects/General/Random/src/X86MAC64/srandom.sharedo and b/src/Objects/General/Random/src/X86MAC64/srandom.sharedo differ

diff --git a/src/Objects/General/Socket/src/X86MAC64/.Depend b/src/Objects/General/Socket/src/X86MAC64/.Depend
index 0b3de2b..36b4105 100644 (file)
--- a/src/Objects/General/Socket/src/X86MAC64/.Depend
+++ b/src/Objects/General/Socket/src/X86MAC64/.Depend
@@ -1,47 +1,2 @@
-socketClient.o: socketClient.c ../inc/Socket.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/sys/types.h /usr/include/sys/socket.h \
-  /usr/include/machine/_param.h /usr/include/i386/_param.h \
-  /usr/include/netinet/in.h /usr/include/stdint.h \
-  /usr/include/netinet6/in6.h /usr/include/netdb.h
-socketServer.o: socketServer.c ../inc/Socket.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/sys/types.h /usr/include/sys/socket.h \
-  /usr/include/machine/_param.h /usr/include/i386/_param.h \
-  /usr/include/netinet/in.h /usr/include/stdint.h \
-  /usr/include/netinet6/in6.h /usr/include/netdb.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h
+X86MAC64/socketClient.o:socketClient.o
+X86MAC64/socketServer.o:socketServer.o

diff --git a/src/Objects/General/Socket/src/X86MAC64/libSocket.a b/src/Objects/General/Socket/src/X86MAC64/libSocket.a
index d8872dc..710f0e2 100644 (file)
Binary files a/src/Objects/General/Socket/src/X86MAC64/libSocket.a and b/src/Objects/General/Socket/src/X86MAC64/libSocket.a differ

diff --git a/src/Objects/General/Socket/src/X86MAC64/libSocket.debug.a b/src/Objects/General/Socket/src/X86MAC64/libSocket.debug.a
index 715891a..ad59a47 100644 (file)
Binary files a/src/Objects/General/Socket/src/X86MAC64/libSocket.debug.a and b/src/Objects/General/Socket/src/X86MAC64/libSocket.debug.a differ

diff --git a/src/Objects/General/Socket/src/X86MAC64/libSocket.so b/src/Objects/General/Socket/src/X86MAC64/libSocket.so
index 84a1f69..5fe3472 100755 (executable)
Binary files a/src/Objects/General/Socket/src/X86MAC64/libSocket.so and b/src/Objects/General/Socket/src/X86MAC64/libSocket.so differ

diff --git a/src/Objects/General/Socket/src/X86MAC64/socketClient.sharedo b/src/Objects/General/Socket/src/X86MAC64/socketClient.sharedo
index d104d39..95ab711 100644 (file)
Binary files a/src/Objects/General/Socket/src/X86MAC64/socketClient.sharedo and b/src/Objects/General/Socket/src/X86MAC64/socketClient.sharedo differ

diff --git a/src/Objects/General/Socket/src/X86MAC64/socketServer.sharedo b/src/Objects/General/Socket/src/X86MAC64/socketServer.sharedo
index 42e7ab4..24a68d5 100644 (file)
Binary files a/src/Objects/General/Socket/src/X86MAC64/socketServer.sharedo and b/src/Objects/General/Socket/src/X86MAC64/socketServer.sharedo differ

diff --git a/src/Objects/General/SpecialNumber/src/X86MAC64/.Depend b/src/Objects/General/SpecialNumber/src/X86MAC64/.Depend
index 1881d62..9d12681 100644 (file)
--- a/src/Objects/General/SpecialNumber/src/X86MAC64/.Depend
+++ b/src/Objects/General/SpecialNumber/src/X86MAC64/.Depend
@@ -1,17 +1 @@
-pow2nn.o: pow2nn.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/SpecialNumber.h
+X86MAC64/pow2nn.o:pow2nn.o

diff --git a/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.a b/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.a
index b59edee..176c62a 100644 (file)
Binary files a/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.a and b/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.a differ

diff --git a/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.debug.a b/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.debug.a
index 401bb7d..1c9cecf 100644 (file)
Binary files a/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.debug.a and b/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.debug.a differ

diff --git a/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.so b/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.so
index 320dc0d..5701f67 100755 (executable)
Binary files a/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.so and b/src/Objects/General/SpecialNumber/src/X86MAC64/libSpecialNumber.so differ

diff --git a/src/Objects/General/SpecialNumber/src/X86MAC64/pow2nn.sharedo b/src/Objects/General/SpecialNumber/src/X86MAC64/pow2nn.sharedo
index 8667115..ca7e4cb 100644 (file)
Binary files a/src/Objects/General/SpecialNumber/src/X86MAC64/pow2nn.sharedo and b/src/Objects/General/SpecialNumber/src/X86MAC64/pow2nn.sharedo differ

diff --git a/src/Objects/General/String/src/X86MAC64/.Depend b/src/Objects/General/String/src/X86MAC64/.Depend
index 0d40a19..3e25fed 100644 (file)
--- a/src/Objects/General/String/src/X86MAC64/.Depend
+++ b/src/Objects/General/String/src/X86MAC64/.Depend
@@ -1,75 +1,4 @@
-stringGet.o: stringGet.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h ../inc/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/String.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h
-stringGetFromFile.o: stringGetFromFile.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h ../inc/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/String.h
-stringIsSame.o: stringIsSame.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/String.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-stringUtil.o: stringUtil.c /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/String.h
+X86MAC64/stringGet.o:stringGet.o
+X86MAC64/stringGetFromFile.o:stringGetFromFile.o
+X86MAC64/stringIsSame.o:stringIsSame.o
+X86MAC64/stringUtil.o:stringUtil.o

diff --git a/src/Objects/General/String/src/X86MAC64/libString.a b/src/Objects/General/String/src/X86MAC64/libString.a
new file mode 100644 (file)
index 0000000..b3477ee
Binary files /dev/null and b/src/Objects/General/String/src/X86MAC64/libString.a differ

diff --git a/src/Objects/General/String/src/X86MAC64/libString.debug.a b/src/Objects/General/String/src/X86MAC64/libString.debug.a
index 0aa6d9d..7113548 100644 (file)
Binary files a/src/Objects/General/String/src/X86MAC64/libString.debug.a and b/src/Objects/General/String/src/X86MAC64/libString.debug.a differ

diff --git a/src/Objects/General/String/src/X86MAC64/stringGet.sharedo b/src/Objects/General/String/src/X86MAC64/stringGet.sharedo
index d6558c3..286f1f0 100644 (file)
Binary files a/src/Objects/General/String/src/X86MAC64/stringGet.sharedo and b/src/Objects/General/String/src/X86MAC64/stringGet.sharedo differ

diff --git a/src/Objects/General/String/src/X86MAC64/stringGetFromFile.sharedo b/src/Objects/General/String/src/X86MAC64/stringGetFromFile.sharedo
index 409f21e..657eb03 100644 (file)
Binary files a/src/Objects/General/String/src/X86MAC64/stringGetFromFile.sharedo and b/src/Objects/General/String/src/X86MAC64/stringGetFromFile.sharedo differ

diff --git a/src/Objects/General/String/src/X86MAC64/stringIsSame.sharedo b/src/Objects/General/String/src/X86MAC64/stringIsSame.sharedo
index 3884118..a0f4d52 100644 (file)
Binary files a/src/Objects/General/String/src/X86MAC64/stringIsSame.sharedo and b/src/Objects/General/String/src/X86MAC64/stringIsSame.sharedo differ

diff --git a/src/Objects/General/String/src/X86MAC64/stringUtil.sharedo b/src/Objects/General/String/src/X86MAC64/stringUtil.sharedo
index 006124c..b4e0e92 100644 (file)
Binary files a/src/Objects/General/String/src/X86MAC64/stringUtil.sharedo and b/src/Objects/General/String/src/X86MAC64/stringUtil.sharedo differ

diff --git a/src/Objects/General/Vector/src/X86MAC64/.Depend b/src/Objects/General/Vector/src/X86MAC64/.Depend
index 6464323..2e199e5 100644 (file)
--- a/src/Objects/General/Vector/src/X86MAC64/.Depend
+++ b/src/Objects/General/Vector/src/X86MAC64/.Depend
@@ -1,76 +1,4 @@
-Vector.o: Vector.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Vector.h
-VectorRead.o: VectorRead.c /Applications/Eos.app/Eos/include/String.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /Applications/Eos.app/Eos/include/File.h \
-  ../inc/Vector.h
-VectorScalarProduct.o: VectorScalarProduct.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/Vector.h
-lVectorSpline2D.o: lVectorSpline2D.c /usr/include/stdlib.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/stdio.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/Vector.h
+X86MAC64/Vector.o:Vector.o
+X86MAC64/VectorRead.o:VectorRead.o
+X86MAC64/VectorScalarProduct.o:VectorScalarProduct.o
+X86MAC64/lVectorSpline2D.o:lVectorSpline2D.o

diff --git a/src/Objects/General/Vector/src/X86MAC64/Vector.sharedo b/src/Objects/General/Vector/src/X86MAC64/Vector.sharedo
index b460542..77f04a2 100644 (file)
Binary files a/src/Objects/General/Vector/src/X86MAC64/Vector.sharedo and b/src/Objects/General/Vector/src/X86MAC64/Vector.sharedo differ

diff --git a/src/Objects/General/Vector/src/X86MAC64/VectorRead.sharedo b/src/Objects/General/Vector/src/X86MAC64/VectorRead.sharedo
index 657f204..2c6593f 100644 (file)
Binary files a/src/Objects/General/Vector/src/X86MAC64/VectorRead.sharedo and b/src/Objects/General/Vector/src/X86MAC64/VectorRead.sharedo differ

diff --git a/src/Objects/General/Vector/src/X86MAC64/VectorScalarProduct.sharedo b/src/Objects/General/Vector/src/X86MAC64/VectorScalarProduct.sharedo
index 4b98df6..c7e9fcb 100644 (file)
Binary files a/src/Objects/General/Vector/src/X86MAC64/VectorScalarProduct.sharedo and b/src/Objects/General/Vector/src/X86MAC64/VectorScalarProduct.sharedo differ

diff --git a/src/Objects/General/Vector/src/X86MAC64/lVectorSpline2D.sharedo b/src/Objects/General/Vector/src/X86MAC64/lVectorSpline2D.sharedo
index e63109c..bb33148 100644 (file)
Binary files a/src/Objects/General/Vector/src/X86MAC64/lVectorSpline2D.sharedo and b/src/Objects/General/Vector/src/X86MAC64/lVectorSpline2D.sharedo differ

diff --git a/src/Objects/General/Vector/src/X86MAC64/libVector.a b/src/Objects/General/Vector/src/X86MAC64/libVector.a
index ce24620..c626d4f 100644 (file)
Binary files a/src/Objects/General/Vector/src/X86MAC64/libVector.a and b/src/Objects/General/Vector/src/X86MAC64/libVector.a differ

diff --git a/src/Objects/General/Vector/src/X86MAC64/libVector.debug.a b/src/Objects/General/Vector/src/X86MAC64/libVector.debug.a
index e8376ea..042e565 100644 (file)
Binary files a/src/Objects/General/Vector/src/X86MAC64/libVector.debug.a and b/src/Objects/General/Vector/src/X86MAC64/libVector.debug.a differ

diff --git a/src/Objects/General/dummy/src/X86MAC64/.Depend b/src/Objects/General/dummy/src/X86MAC64/.Depend
index cef0895..fd39f7b 100644 (file)
--- a/src/Objects/General/dummy/src/X86MAC64/.Depend
+++ b/src/Objects/General/dummy/src/X86MAC64/.Depend
@@ -1,5 +1 @@
-ctype_b.o: ctype_b.c /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h
+X86MAC64/ctype_b.o:ctype_b.o

diff --git a/src/Objects/General/dummy/src/X86MAC64/ctype_b.sharedo b/src/Objects/General/dummy/src/X86MAC64/ctype_b.sharedo
index bb65069..313d7e1 100644 (file)
Binary files a/src/Objects/General/dummy/src/X86MAC64/ctype_b.sharedo and b/src/Objects/General/dummy/src/X86MAC64/ctype_b.sharedo differ

diff --git a/src/Objects/General/dummy/src/X86MAC64/libdummy.a b/src/Objects/General/dummy/src/X86MAC64/libdummy.a
index d8b7503..fc610e2 100644 (file)
Binary files a/src/Objects/General/dummy/src/X86MAC64/libdummy.a and b/src/Objects/General/dummy/src/X86MAC64/libdummy.a differ

diff --git a/src/Objects/General/dummy/src/X86MAC64/libdummy.debug.a b/src/Objects/General/dummy/src/X86MAC64/libdummy.debug.a
index 197da9d..ac0bbbb 100644 (file)
Binary files a/src/Objects/General/dummy/src/X86MAC64/libdummy.debug.a and b/src/Objects/General/dummy/src/X86MAC64/libdummy.debug.a differ

diff --git a/src/Objects/General/dummy/src/X86MAC64/libdummy.so b/src/Objects/General/dummy/src/X86MAC64/libdummy.so
index 39d461b..88ca25c 100755 (executable)
Binary files a/src/Objects/General/dummy/src/X86MAC64/libdummy.so and b/src/Objects/General/dummy/src/X86MAC64/libdummy.so differ

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/.Depend b/src/Objects/General/eosCuda/src/X86MAC64/.Depend
new file mode 100644 (file)
index 0000000..18dd30a
--- /dev/null
+++ b/src/Objects/General/eosCuda/src/X86MAC64/.Depend
@@ -0,0 +1 @@
+X86MAC64/eosCuda.o:eosCuda.o

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/.Source b/src/Objects/General/eosCuda/src/X86MAC64/.Source
new file mode 100644 (file)
index 0000000..151bf37
--- /dev/null
+++ b/src/Objects/General/eosCuda/src/X86MAC64/.Source
@@ -0,0 +1,28 @@
+SRC = \
+eosCuda.c \
+
+OBJ = \
+eosCuda.o \
+
+SHAREDOBJ = \
+eosCuda.sharedo \
+
+REALOBJ = \
+X86MAC64/eosCuda.o \
+
+REALSHAREDOBJ = \
+X86MAC64/eosCuda.sharedo \
+
+OBJDEBUG = \
+eosCuda.debugo \
+
+REALOBJDEBUG = \
+X86MAC64/eosCuda.debugo \
+
+OBJCUDAGDB = \
+eosCuda.cudagdb.o \
+
+REALOBJCUDAGDB = \
+X86MAC64/eosCuda.cudagdb.o \
+
+

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/Makefile b/src/Objects/General/eosCuda/src/X86MAC64/Makefile
new file mode 100755 (executable)
index 0000000..28e9069
--- /dev/null
+++ b/src/Objects/General/eosCuda/src/X86MAC64/Makefile
@@ -0,0 +1,34 @@
+SHELL=/bin/ksh
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineObject.inc
+
+include .Source
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.CHeader
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.CCHeader
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.Wish
+
+LIBNAME=lib$(OBJECTNAME).a
+SHAREDLIB=lib$(OBJECTNAME).so
+LIBNAMEDEBUG=lib$(OBJECTNAME).debug.a
+LIBNAMECUDAGDB=lib$(OBJECTNAME).cudagdb.a
+
+$(LIBNAME): $(OBJ)
+       @echo LIBNAME:$(LIBNAME)
+       $(AR) rs $(LIBNAME) $(OBJ)
+
+$(SHAREDLIB): $(SHAREDOBJ)
+       @COMPILEDOBJ=`ls $(SHAREDOBJ)` ; echo "#### Compiled Objects"; echo $${COMPILEDOBJ};  echo "################"; \
+       $(SHARED) $(SHAREDLIB) $${COMPILEDOBJ} 
+
+$(LIBNAMEDEBUG): $(OBJDEBUG)
+       @echo LIBNAME:$(LIBNAMEDEBUG)
+       $(AR) rs $(LIBNAMEDEBUG) $(OBJDEBUG)
+
+$(LIBNAMECUDAGDB): $(OBJCUDAGDB)
+       @echo LIBNAME:$(LIBNAMECUDAGDB)
+       $(AR) rs $(LIBNAMECUDAGDB) $(OBJCUDAGDB)
+
+include .Depend
+

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/X86MAC64 b/src/Objects/General/eosCuda/src/X86MAC64/X86MAC64
new file mode 120000 (symlink)
index 0000000..66f16a7
--- /dev/null
+++ b/src/Objects/General/eosCuda/src/X86MAC64/X86MAC64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86MAC64/src/Objects/General/eosCuda/src/X86MAC64
\ No newline at end of file

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/eosCuda.sharedo b/src/Objects/General/eosCuda/src/X86MAC64/eosCuda.sharedo
new file mode 100644 (file)
index 0000000..0409ab3
Binary files /dev/null and b/src/Objects/General/eosCuda/src/X86MAC64/eosCuda.sharedo differ

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.a b/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.a
new file mode 100644 (file)
index 0000000..8459ef1
Binary files /dev/null and b/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.a differ

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.debug.a b/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.debug.a
new file mode 100644 (file)
index 0000000..1ad8d16
Binary files /dev/null and b/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.debug.a differ

diff --git a/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.so b/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.so
new file mode 100755 (executable)
index 0000000..96baafb
Binary files /dev/null and b/src/Objects/General/eosCuda/src/X86MAC64/libeosCuda.so differ

diff --git a/src/Objects/General/eosPThread/src/X86MAC64/.Depend b/src/Objects/General/eosPThread/src/X86MAC64/.Depend
index ca0748f..4e4cbd4 100755 (executable)
--- a/src/Objects/General/eosPThread/src/X86MAC64/.Depend
+++ b/src/Objects/General/eosPThread/src/X86MAC64/.Depend
@@ -1,108 +1,5 @@
-eosPThread.o: eosPThread.c ../inc/eosPThread.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h
-eosPThreadCreate.o: eosPThreadCreate.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/eosPThread.h \
-  /usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h
-eosPThreadInit.o: eosPThreadInit.c \
-  /Applications/Eos.app/Eos/include/Memory.h /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/eosPThread.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h
-eosPThreadJoin.o: eosPThreadJoin.c ../inc/eosPThread.h \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h
-eosPThreadMutex.o: eosPThreadMutex.c \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/pthread.h \
-  /usr/include/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/sys/_structs.h ../inc/eosPThread.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/errno.h \
-  /usr/include/sys/errno.h
+X86MAC64/eosPThread.o:eosPThread.o
+X86MAC64/eosPThreadCreate.o:eosPThreadCreate.o
+X86MAC64/eosPThreadInit.o:eosPThreadInit.o
+X86MAC64/eosPThreadJoin.o:eosPThreadJoin.o
+X86MAC64/eosPThreadMutex.o:eosPThreadMutex.o

diff --git a/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadCreate.sharedo b/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadCreate.sharedo
index 2d3798a..7cdd4d9 100644 (file)
Binary files a/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadCreate.sharedo and b/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadCreate.sharedo differ

diff --git a/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadInit.sharedo b/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadInit.sharedo
index 2689a41..9647c8c 100644 (file)
Binary files a/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadInit.sharedo and b/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadInit.sharedo differ

diff --git a/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadJoin.sharedo b/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadJoin.sharedo
index 9523c26..e8518a8 100644 (file)
Binary files a/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadJoin.sharedo and b/src/Objects/General/eosPThread/src/X86MAC64/eosPThreadJoin.sharedo differ

diff --git a/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.a b/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.a
index 566df8e..e33f3a5 100644 (file)
Binary files a/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.a and b/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.a differ

diff --git a/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.debug.a b/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.debug.a
index 9ce0bcf..cb1ed52 100644 (file)
Binary files a/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.debug.a and b/src/Objects/General/eosPThread/src/X86MAC64/libeosPThread.debug.a differ

diff --git a/src/Objects/General/eosPoint/src/X86MAC64/.Depend b/src/Objects/General/eosPoint/src/X86MAC64/.Depend
index 5406ffb..dae6e2d 100644 (file)
--- a/src/Objects/General/eosPoint/src/X86MAC64/.Depend
+++ b/src/Objects/General/eosPoint/src/X86MAC64/.Depend
@@ -1 +1 @@
-eosPointRead.o: eosPointRead.c
+X86MAC64/eosPointRead.o:eosPointRead.o

diff --git a/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.a b/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.a
index 54e2faf..eeb914f 100644 (file)
Binary files a/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.a and b/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.a differ

diff --git a/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.debug.a b/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.debug.a
index 9aa1189..02fccb9 100644 (file)
Binary files a/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.debug.a and b/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.debug.a differ

diff --git a/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.so b/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.so
index 4d4d28c..76a15d7 100755 (executable)
Binary files a/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.so and b/src/Objects/General/eosPoint/src/X86MAC64/libeosPoint.so differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/.Depend b/src/Objects/MachineManip/hf2000/src/X86MAC64/.Depend
index 96421ff..70786f3 100644 (file)
--- a/src/Objects/MachineManip/hf2000/src/X86MAC64/.Depend
+++ b/src/Objects/MachineManip/hf2000/src/X86MAC64/.Depend
@@ -1,252 +1,8 @@
-hf2000Close.o: hf2000Close.c ../inc/hf2000.h /usr/include/sys/types.h \
-  /usr/include/sys/appleapiopts.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/sys/stat.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/fcntl.h \
-  /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
-  /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /usr/include/_types.h /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h
-hf2000Command.o: hf2000Command.c ../inc/hf2000.h /usr/include/sys/types.h \
-  /usr/include/sys/appleapiopts.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/sys/stat.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/fcntl.h \
-  /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
-  /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /usr/include/_types.h /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h
-hf2000Init.o: hf2000Init.c ../inc/hf2000.h /usr/include/sys/types.h \
-  /usr/include/sys/appleapiopts.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/sys/stat.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/fcntl.h \
-  /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
-  /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /usr/include/_types.h /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/alloca.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/string.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/Socket.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/sys/socket.h \
-  /usr/include/machine/_param.h /usr/include/i386/_param.h \
-  /usr/include/netinet/in.h /usr/include/stdint.h \
-  /usr/include/netinet6/in6.h /usr/include/netdb.h
-hf2000Read.o: hf2000Read.c /usr/include/unistd.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/sys/unistd.h \
-  /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
-  /usr/include/sys/select.h /usr/include/sys/appleapiopts.h \
-  /usr/include/sys/_structs.h /usr/include/sys/_select.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  ../inc/hf2000.h /usr/include/sys/types.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/stat.h \
-  /usr/include/fcntl.h /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
-  /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h
-hf2000Write.o: hf2000Write.c /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h ../inc/hf2000.h \
-  /usr/include/sys/types.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/sys/_types.h \
-  /usr/include/machine/_types.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/sys/stat.h /usr/include/fcntl.h /usr/include/sys/fcntl.h \
-  /usr/include/termios.h /usr/include/sys/termios.h \
-  /usr/include/sys/ttycom.h /usr/include/sys/ioccom.h \
-  /usr/include/sys/ttydefaults.h /usr/include/_types.h \
-  /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/alloca.h /usr/include/unistd.h /usr/include/sys/unistd.h \
-  /usr/include/sys/select.h /usr/include/sys/_select.h
-lhf2000LenzCurrent.o: lhf2000LenzCurrent.c ../inc/hf2000.h \
-  /usr/include/sys/types.h /usr/include/sys/appleapiopts.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/sys/stat.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/fcntl.h \
-  /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
-  /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /usr/include/_types.h /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  lhf2000LenzCurrent.h ../inc/hf2000.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/alloca.h /usr/include/unistd.h /usr/include/sys/unistd.h \
-  /usr/include/sys/select.h /usr/include/sys/_select.h
-lhf2000SpecimenPosition.o: lhf2000SpecimenPosition.c ../inc/hf2000.h \
-  /usr/include/sys/types.h /usr/include/sys/appleapiopts.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/machine/types.h \
-  /usr/include/i386/types.h /usr/include/i386/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
-  /usr/include/sys/stat.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/fcntl.h \
-  /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
-  /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /usr/include/_types.h /usr/include/stdio.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  lhf2000SpecimenPosition.h ../inc/hf2000.h \
-  /Applications/Eos.app/Eos/include/genUtil.h /usr/include/math.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/string.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/alloca.h /usr/include/unistd.h /usr/include/sys/unistd.h \
-  /usr/include/sys/select.h /usr/include/sys/_select.h
-ltkhf2000.o: ltkhf2000.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /usr/include/math.h ../inc/hf2000.h /usr/include/sys/types.h \
-  /usr/include/sys/stat.h /usr/include/fcntl.h /usr/include/sys/fcntl.h \
-  /usr/include/termios.h /usr/include/sys/termios.h \
-  /usr/include/sys/ttycom.h /usr/include/sys/ioccom.h \
-  /usr/include/sys/ttydefaults.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
-  lhf2000SpecimenPosition.h ../inc/hf2000.h lhf2000LenzCurrent.h
+X86MAC64/hf2000Close.o:hf2000Close.o
+X86MAC64/hf2000Command.o:hf2000Command.o
+X86MAC64/hf2000Init.o:hf2000Init.o
+X86MAC64/hf2000Read.o:hf2000Read.o
+X86MAC64/hf2000Write.o:hf2000Write.o
+X86MAC64/lhf2000LenzCurrent.o:lhf2000LenzCurrent.o
+X86MAC64/lhf2000SpecimenPosition.o:lhf2000SpecimenPosition.o
+X86MAC64/ltkhf2000.o:ltkhf2000.o

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Close.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Close.sharedo
index ee18759..db5596c 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Close.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Close.sharedo differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Command.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Command.sharedo
index 693fbad..cd48eec 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Command.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Command.sharedo differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Init.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Init.sharedo
index 2b4f6c6..b50b538 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Init.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Init.sharedo differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Read.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Read.sharedo
index 56bfccf..bb94f9b 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Read.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Read.sharedo differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Write.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Write.sharedo
index 09cb70c..2111974 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Write.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/hf2000Write.sharedo differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000LenzCurrent.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000LenzCurrent.sharedo
index e090ab1..e5178a1 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000LenzCurrent.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000LenzCurrent.sharedo differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000SpecimenPosition.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000SpecimenPosition.sharedo
index 22b3ef3..770d174 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000SpecimenPosition.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/lhf2000SpecimenPosition.sharedo differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.a b/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.a
index 1fece06..0e2d6c8 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.a and b/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.a differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.debug.a b/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.debug.a
index ede57e7..305bad4 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.debug.a and b/src/Objects/MachineManip/hf2000/src/X86MAC64/libhf2000.debug.a differ

diff --git a/src/Objects/MachineManip/hf2000/src/X86MAC64/ltkhf2000.sharedo b/src/Objects/MachineManip/hf2000/src/X86MAC64/ltkhf2000.sharedo
index 8026453..5aa19b1 100644 (file)
Binary files a/src/Objects/MachineManip/hf2000/src/X86MAC64/ltkhf2000.sharedo and b/src/Objects/MachineManip/hf2000/src/X86MAC64/ltkhf2000.sharedo differ

diff --git a/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/.Depend b/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/.Depend
index 414b615..870f3b8 100644 (file)
--- a/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/.Depend
+++ b/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/clusterLog2ToLog.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterLog2ToLog.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ clusterLog2ToLog.o: clusterLog2ToLog.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/clusterLog2ToLog.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterLog2ToLog.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Cluster.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/clusterLog2ToLog.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterLog2ToLog.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/clusterLog2ToLog.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/clusterLog2ToLog.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/clusterLog2ToLog.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/clusterLog2ToLog.h

diff --git a/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/Makefile b/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/Makefile
+++ b/src/Tools/Cluster/clusterLog2ToLog/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/.Depend b/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/.Depend
index ad31053..1ddde68 100644 (file)
--- a/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/.Depend
+++ b/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/clusterLogASCII2Binary.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterLogASCII2Binary.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,20 +47,38 @@ clusterLogASCII2Binary.o: clusterLogASCII2Binary.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/clusterLogASCII2Binary.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterLogASCII2Binary.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Cluster.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -54,28 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/clusterLogASCII2Binary.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterLogASCII2Binary.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -84,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/clusterLogASCII2Binary.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/clusterLogASCII2Binary.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/clusterLogASCII2Binary.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/clusterLogASCII2Binary.h

diff --git a/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/Makefile b/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/Makefile
+++ b/src/Tools/Cluster/clusterLogASCII2Binary/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Cluster/clusterShow/src/X86MAC64/.Depend b/src/Tools/Cluster/clusterShow/src/X86MAC64/.Depend
index e4e3be0..8e0a301 100644 (file)
--- a/src/Tools/Cluster/clusterShow/src/X86MAC64/.Depend
+++ b/src/Tools/Cluster/clusterShow/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/clusterShow.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterShow.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,25 +47,41 @@ clusterShow.o: clusterShow.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/clusterShow.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterShow.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
@@ -60,27 +91,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/clusterShow.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/clusterShow.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -89,32 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/clusterShow.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/clusterShow.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/clusterShow.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/clusterShow.h

diff --git a/src/Tools/Cluster/clusterShow/src/X86MAC64/Makefile b/src/Tools/Cluster/clusterShow/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Cluster/clusterShow/src/X86MAC64/Makefile
+++ b/src/Tools/Cluster/clusterShow/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Coord/coordRotation/src/X86MAC64/.Depend b/src/Tools/Coord/coordRotation/src/X86MAC64/.Depend
index d052d12..2e83a5d 100644 (file)
--- a/src/Tools/Coord/coordRotation/src/X86MAC64/.Depend
+++ b/src/Tools/Coord/coordRotation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/coordRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/coordRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ coordRotation.o: coordRotation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/coordRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/coordRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -54,27 +88,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/coordRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/coordRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -83,34 +132,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/coordRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/coordRotation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/coordRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/coordRotation.h

diff --git a/src/Tools/Coord/coordRotation/src/X86MAC64/Makefile b/src/Tools/Coord/coordRotation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Coord/coordRotation/src/X86MAC64/Makefile
+++ b/src/Tools/Coord/coordRotation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Coord/coordRotation/src/X86MAC64/coordRotation b/src/Tools/Coord/coordRotation/src/X86MAC64/coordRotation
index 3ad2185..41f0664 100755 (executable)
Binary files a/src/Tools/Coord/coordRotation/src/X86MAC64/coordRotation and b/src/Tools/Coord/coordRotation/src/X86MAC64/coordRotation differ

diff --git a/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/.Depend b/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/.Depend
index 05bf3a1..b8b9022 100644 (file)
--- a/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/.Depend
+++ b/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pointsSetToPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pointsSetToPDB.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pointsSetToPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pointsSetToPDB.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pointsSetToPDB.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pointsSetToPDB.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pointsSetToPDB.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pointsSetToPDB.h

diff --git a/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/Makefile b/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/Makefile
+++ b/src/Tools/Coord/pointsSetToPDB/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/.Depend
index 8c017d2..b6c8be4 100644 (file)
--- a/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/.Depend
@@ -4,853 +4,137 @@ dcdAtomChangeDistanceFromAtom.o: dcdAtomChangeDistanceFromAtom.cc \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/dcdAtomChangeDistanceFromAtom.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdAtomChangeDistanceFromAtom.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \
+  /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
+  /usr/include/_wctype.h /usr/include/sys/_types/_wint_t.h \
+  /usr/include/_types/_wctype_t.h /usr/include/ctype.h \
+  /usr/include/runetype.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__locale \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwctype \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype \
+  /usr/include/wctype.h /usr/include/_types/_wctrans_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/initializer_list \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstddef \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/type_traits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/typeinfo \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/exception \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdint \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/new \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/limits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__undef_min_max \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/stdexcept \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/mutex \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__mutex_base \
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-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/.Depend
index f34e588..df20e39 100644 (file)
--- a/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/.Depend
@@ -4,853 +4,137 @@ dcdAtomDistanceDistribution.o: dcdAtomDistanceDistribution.cc \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/dcdAtomDistanceDistribution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdAtomDistanceDistribution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \
+  /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
+  /usr/include/_wctype.h /usr/include/sys/_types/_wint_t.h \
+  /usr/include/_types/_wctype_t.h /usr/include/ctype.h \
+  /usr/include/runetype.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__locale \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwctype \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype \
+  /usr/include/wctype.h /usr/include/_types/_wctrans_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/initializer_list \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstddef \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/type_traits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/typeinfo \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/exception \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdint \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/new \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/limits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__undef_min_max \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/stdexcept \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/mutex \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__mutex_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/chrono \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ctime \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ratio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/climits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
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-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
+  /usr/include/sys/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/system_error \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cerrno \
+  /usr/include/errno.h /usr/include/sys/errno.h \
+  /usr/include/sys/_types/_errno_t.h /usr/include/pthread.h \
+  /usr/include/pthread_impl.h /usr/include/sched.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_mach_port_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/functional \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_03 \
+  /usr/include/locale.h /usr/include/_locale.h /usr/include/xlocale.h \
+  /usr/include/_xlocale.h /usr/include/xlocale/_ctype.h \
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+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/streambuf \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/istream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/locale \
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+  /usr/include/nl_types.h /usr/include/sys/types.h \
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-  /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-dcdAtomDistanceDistribution.o: dcdAtomDistanceDistribution.cc \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/dcdAtomDistanceDistribution.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/.Depend
index 99a6a9c..6bff2e3 100644 (file)
--- a/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdCompareCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdCompareCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdCompareCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdCompareCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,32 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/dcdCompareCA.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/dcdCompareCA.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/dcdCompareCA.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/dcdCompareCA.h

diff --git a/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdCompareCA/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/.Depend
index 6a55b77..9c83f2d 100644 (file)
--- a/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/.Depend
@@ -4,853 +4,137 @@ dcdDistanceAtomBetweenAtom.o: dcdDistanceAtomBetweenAtom.cc \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/dcdDistanceAtomBetweenAtom.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdDistanceAtomBetweenAtom.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \
+  /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
+  /usr/include/_wctype.h /usr/include/sys/_types/_wint_t.h \
+  /usr/include/_types/_wctype_t.h /usr/include/ctype.h \
+  /usr/include/runetype.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__locale \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwctype \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype \
+  /usr/include/wctype.h /usr/include/_types/_wctrans_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/initializer_list \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstddef \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/type_traits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple_03 \
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-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/.Depend
index caf1349..ec69500 100644 (file)
--- a/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/.Depend
@@ -3,838 +3,137 @@ dcdFilePrint.o: dcdFilePrint.cc /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdFilePrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdFilePrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \
+  /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
+  /usr/include/_wctype.h /usr/include/sys/_types/_wint_t.h \
+  /usr/include/_types/_wctype_t.h /usr/include/ctype.h \
+  /usr/include/runetype.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__locale \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwctype \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype \
+  /usr/include/wctype.h /usr/include/_types/_wctrans_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/initializer_list \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstddef \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/type_traits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/typeinfo \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/exception \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdint \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/new \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/limits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__undef_min_max \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/stdexcept \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/mutex \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__mutex_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/chrono \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ctime \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ratio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/climits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
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-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
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-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
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-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
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-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
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-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
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-  /usr/include/c++/4.2.1/bits/basic_ios.h \
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-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
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-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
+  /usr/include/sys/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/system_error \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cerrno \
+  /usr/include/errno.h /usr/include/sys/errno.h \
+  /usr/include/sys/_types/_errno_t.h /usr/include/pthread.h \
+  /usr/include/pthread_impl.h /usr/include/sched.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_mach_port_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/functional \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_03 \
+  /usr/include/locale.h /usr/include/_locale.h /usr/include/xlocale.h \
+  /usr/include/_xlocale.h /usr/include/xlocale/_ctype.h \
+  /usr/include/xlocale/__wctype.h /usr/include/xlocale/_stdio.h \
+  /usr/include/xlocale/_stdlib.h /usr/include/xlocale/_time.h \
+  /usr/include/xlocale/_wchar.h /usr/include/xlocale/_wctype.h \
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-dcdFilePrint.o: dcdFilePrint.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdFilePrint.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-dcdFilePrint.o: dcdFilePrint.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdFilePrint.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdFilePrint/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdInfo/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdInfo/src/X86MAC64/.Depend
index 72d59e7..60f4826 100644 (file)
--- a/src/Tools/DCDFile/dcdInfo/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdInfo/src/X86MAC64/.Depend
@@ -3,838 +3,137 @@ dcdInfo.o: dcdInfo.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
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-  /Applications/Eos.app/Eos/include/ctfInfo.h
-dcdInfo.o: dcdInfo.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdInfo/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdInfo/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/.Depend
index 651c376..67f010d 100644 (file)
--- a/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/.Depend
@@ -3,838 +3,137 @@ dcdSelectAtoms.o: dcdSelectAtoms.cc /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdSelectAtoms.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdSelectAtoms.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \
+  /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
+  /usr/include/_wctype.h /usr/include/sys/_types/_wint_t.h \
+  /usr/include/_types/_wctype_t.h /usr/include/ctype.h \
+  /usr/include/runetype.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__locale \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwctype \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype \
+  /usr/include/wctype.h /usr/include/_types/_wctrans_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/initializer_list \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstddef \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/type_traits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/typeinfo \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/exception \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdint \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/new \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/limits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__undef_min_max \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/stdexcept \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/mutex \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__mutex_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/chrono \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ctime \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ratio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/climits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
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-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdSelectAtoms/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/.Depend
index 5da35d6..80afdc6 100644 (file)
--- a/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/.Depend
@@ -3,838 +3,137 @@ dcdSerectAtom.o: dcdSerectAtom.cc /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdSerectAtom.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdSerectAtom.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \
+  /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
+  /usr/include/_wctype.h /usr/include/sys/_types/_wint_t.h \
+  /usr/include/_types/_wctype_t.h /usr/include/ctype.h \
+  /usr/include/runetype.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__locale \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwctype \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype \
+  /usr/include/wctype.h /usr/include/_types/_wctrans_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/initializer_list \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstddef \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/type_traits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tuple_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/typeinfo \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/exception \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdint \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/new \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/limits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__undef_min_max \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_base_03 \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/tuple \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/stdexcept \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/mutex \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__mutex_base \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/chrono \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ctime \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ratio \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/climits \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
+  /usr/include/sys/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/system_error \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cerrno \
+  /usr/include/errno.h /usr/include/sys/errno.h \
+  /usr/include/sys/_types/_errno_t.h /usr/include/pthread.h \
+  /usr/include/pthread_impl.h /usr/include/sched.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_mach_port_t.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/functional \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_03 \
+  /usr/include/locale.h /usr/include/_locale.h /usr/include/xlocale.h \
+  /usr/include/_xlocale.h /usr/include/xlocale/_ctype.h \
+  /usr/include/xlocale/__wctype.h /usr/include/xlocale/_stdio.h \
+  /usr/include/xlocale/_stdlib.h /usr/include/xlocale/_time.h \
+  /usr/include/xlocale/_wchar.h /usr/include/xlocale/_wctype.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/streambuf \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/istream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/locale \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdlib \
+  /usr/include/nl_types.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/_types/_nl_item.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/bitset \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-dcdSerectAtom.o: dcdSerectAtom.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
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-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
-dcdSerectAtom.o: dcdSerectAtom.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dcdSerectAtom.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdSerectAtom/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/.Depend b/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/.Depend
index 339bab9..f181ecb 100644 (file)
--- a/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/.Depend
+++ b/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/.Depend
@@ -3,846 +3,137 @@ dcdTimeSeriesBehavior.o: dcdTimeSeriesBehavior.cc /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/dcdTimeSeriesBehavior.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dcdTimeSeriesBehavior.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/DCDFile.h \
-  /usr/include/c++/4.2.1/iostream /usr/include/c++/4.2.1/bits/c++config.h \
-  /usr/include/c++/4.2.1/bits/os_defines.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /usr/include/c++/4.2.1/bits/cpu_defines.h \
-  /usr/include/c++/4.2.1/ostream /usr/include/c++/4.2.1/ios \
-  /usr/include/c++/4.2.1/iosfwd /usr/include/c++/4.2.1/bits/c++locale.h \
-  /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
-  /usr/include/_locale.h /usr/include/c++/4.2.1/cstring \
-  /usr/include/c++/4.2.1/cstddef \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /usr/include/c++/4.2.1/cstdio /usr/include/c++/4.2.1/cstdarg \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /usr/include/c++/4.2.1/bits/c++io.h /usr/include/c++/4.2.1/bits/gthr.h \
-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios \
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-  /usr/include/c++/4.2.1/bits/gthr-default.h /usr/include/pthread.h \
-  /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/c++/4.2.1/cctype \
-  /usr/include/ctype.h /usr/include/runetype.h \
-  /usr/include/c++/4.2.1/bits/stringfwd.h \
-  /usr/include/c++/4.2.1/bits/postypes.h /usr/include/c++/4.2.1/cwchar \
-  /usr/include/c++/4.2.1/ctime /usr/include/wchar.h \
-  /usr/include/_wctype.h /usr/include/stdint.h \
-  /usr/include/c++/4.2.1/bits/functexcept.h \
-  /usr/include/c++/4.2.1/exception_defines.h \
-  /usr/include/c++/4.2.1/exception \
-  /usr/include/c++/4.2.1/bits/char_traits.h \
-  /usr/include/c++/4.2.1/bits/stl_algobase.h \
-  /usr/include/c++/4.2.1/climits \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
-  /usr/include/c++/4.2.1/bits/stl_pair.h \
-  /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
-  /usr/include/c++/4.2.1/bits/stl_relops.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2.1/bits/concept_check.h \
-  /usr/include/c++/4.2.1/bits/stl_iterator.h \
-  /usr/include/c++/4.2.1/debug/debug.h \
-  /usr/include/c++/4.2.1/bits/localefwd.h \
-  /usr/include/c++/4.2.1/bits/ios_base.h \
-  /usr/include/c++/4.2.1/ext/atomicity.h \
-  /usr/include/c++/4.2.1/bits/atomic_word.h \
-  /usr/include/c++/4.2.1/bits/locale_classes.h \
-  /usr/include/c++/4.2.1/string /usr/include/c++/4.2.1/memory \
-  /usr/include/c++/4.2.1/bits/allocator.h \
-  /usr/include/c++/4.2.1/bits/c++allocator.h \
-  /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
-  /usr/include/c++/4.2.1/bits/stl_construct.h \
-  /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2.1/limits \
-  /usr/include/c++/4.2.1/bits/ostream_insert.h \
-  /usr/include/c++/4.2.1/bits/stl_function.h \
-  /usr/include/c++/4.2.1/bits/basic_string.h \
-  /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
-  /usr/include/c++/4.2.1/bits/stl_heap.h \
-  /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2.1/bits/basic_string.tcc \
-  /usr/include/c++/4.2.1/streambuf \
-  /usr/include/c++/4.2.1/bits/streambuf.tcc \
-  /usr/include/c++/4.2.1/bits/basic_ios.h \
-  /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2.1/bits/locale_facets.h \
-  /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
-  /usr/include/c++/4.2.1/bits/ctype_base.h \
-  /usr/include/c++/4.2.1/bits/ctype_inline.h \
-  /usr/include/c++/4.2.1/bits/codecvt.h \
-  /usr/include/c++/4.2.1/bits/time_members.h \
-  /usr/include/c++/4.2.1/bits/messages_members.h \
-  /usr/include/c++/4.2.1/bits/basic_ios.tcc \
-  /usr/include/c++/4.2.1/bits/ostream.tcc /usr/include/c++/4.2.1/locale \
-  /usr/include/c++/4.2.1/bits/locale_facets.tcc \
-  /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/istream \
-  /usr/include/c++/4.2.1/bits/istream.tcc \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h

diff --git a/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/Makefile b/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/Makefile
+++ b/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/Display2/src/X86MAC64/.Depend b/src/Tools/Integration/Display2/src/X86MAC64/.Depend
index ba0aa4e..4a98d14 100644 (file)
--- a/src/Tools/Integration/Display2/src/X86MAC64/.Depend
+++ b/src/Tools/Integration/Display2/src/X86MAC64/.Depend
@@ -3,21 +3,39 @@ Display2.o: Display2.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
@@ -27,26 +45,48 @@ Display2.o: Display2.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
+  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/blt.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltVector.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltHash.h \
-  /usr/include/inttypes.h /usr/include/stdint.h \
+  /usr/include/inttypes.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltPool.h \
   ../inc/config.h ../inc/../inc/Display2.h \
   /Applications/Eos.app/Eos/include/tkImgFmtMRC.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
   /Applications/Eos.app/Eos/include/tkctfInfo.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -54,27 +94,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Display2.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Display2.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -83,27 +138,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Display2.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Display2.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -112,32 +182,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Display2.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/Display2.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Display2.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/Display2.h

diff --git a/src/Tools/Integration/Display2/src/X86MAC64/Display2 b/src/Tools/Integration/Display2/src/X86MAC64/Display2
index d8d4101..76e0fd2 100755 (executable)
Binary files a/src/Tools/Integration/Display2/src/X86MAC64/Display2 and b/src/Tools/Integration/Display2/src/X86MAC64/Display2 differ

diff --git a/src/Tools/Integration/Display2/src/X86MAC64/Makefile b/src/Tools/Integration/Display2/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/Display2/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/Display2/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/Display3/src/X86MAC64/.Depend b/src/Tools/Integration/Display3/src/X86MAC64/.Depend
index 1ebcf03..f68570e 100644 (file)
--- a/src/Tools/Integration/Display3/src/X86MAC64/.Depend
+++ b/src/Tools/Integration/Display3/src/X86MAC64/.Depend
@@ -1,9 +1 @@
 util.o: util.cc
-util.o: util.cc
-util.o: util.cc
-util.o: util.cc
-util.o: util.cc
-util.o: util.cc
-util.o: util.cc
-util.o: util.cc
-util.o: util.cc

diff --git a/src/Tools/Integration/Display3/src/X86MAC64/Makefile b/src/Tools/Integration/Display3/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/Display3/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/Display3/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/StereoDisplay/src/X86MAC64/Makefile b/src/Tools/Integration/StereoDisplay/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/StereoDisplay/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/StereoDisplay/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/Visualmake/src/X86MAC64/Makefile b/src/Tools/Integration/Visualmake/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/Visualmake/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/Visualmake/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/X86MAC64/.Depend b/src/Tools/Integration/X86MAC64/.Depend
index f6b629e..d7dba25 100644 (file)
--- a/src/Tools/Integration/X86MAC64/.Depend
+++ b/src/Tools/Integration/X86MAC64/.Depend
@@ -1,143 +1,35 @@
-util.o: util.cc /usr/include/stdio.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
-  /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
-util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
-util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
-util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
-util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
-util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
-util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
-util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
 util.o: util.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/Eos.h
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/Eos.h

diff --git a/src/Tools/Integration/X86MAC64/Makefile b/src/Tools/Integration/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/X86MAC64/Makefile
+++ b/src/Tools/Integration/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/ctfDisplay/src/X86MAC64/.Depend b/src/Tools/Integration/ctfDisplay/src/X86MAC64/.Depend
index 76731f7..dd20cdb 100644 (file)
--- a/src/Tools/Integration/ctfDisplay/src/X86MAC64/.Depend
+++ b/src/Tools/Integration/ctfDisplay/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfDisplay.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDisplay.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,51 +47,90 @@ ctfDisplay.o: ctfDisplay.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfDisplay.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDisplay.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
+  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/blt.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltVector.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltHash.h \
-  /usr/include/inttypes.h /usr/include/stdint.h \
+  /usr/include/inttypes.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltPool.h \
   /Applications/Eos.app/Eos/include/tkImgFmtMRC.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
   /Applications/Eos.app/Eos/include/tkctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -84,27 +138,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfDisplay.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDisplay.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -113,32 +182,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfDisplay.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDisplay.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfDisplay.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDisplay.h

diff --git a/src/Tools/Integration/ctfDisplay/src/X86MAC64/Makefile b/src/Tools/Integration/ctfDisplay/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/ctfDisplay/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/ctfDisplay/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/ctfDisplay/src/X86MAC64/ctfDisplay b/src/Tools/Integration/ctfDisplay/src/X86MAC64/ctfDisplay
index 23fc924..ff14034 100755 (executable)
Binary files a/src/Tools/Integration/ctfDisplay/src/X86MAC64/ctfDisplay and b/src/Tools/Integration/ctfDisplay/src/X86MAC64/ctfDisplay differ

diff --git a/src/Tools/Integration/imagesClustering/src/X86MAC64/.Depend b/src/Tools/Integration/imagesClustering/src/X86MAC64/.Depend
index ba8742a..c593792 100644 (file)
--- a/src/Tools/Integration/imagesClustering/src/X86MAC64/.Depend
+++ b/src/Tools/Integration/imagesClustering/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/imagesClustering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/imagesClustering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/imagesClustering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/imagesClustering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/imagesClustering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/imagesClustering.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/imagesClustering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/imagesClustering.h

diff --git a/src/Tools/Integration/imagesClustering/src/X86MAC64/Makefile b/src/Tools/Integration/imagesClustering/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/imagesClustering/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/imagesClustering/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/imagesView/src/X86MAC64/.Depend b/src/Tools/Integration/imagesView/src/X86MAC64/.Depend
index 82aaaa0..3342088 100644 (file)
--- a/src/Tools/Integration/imagesView/src/X86MAC64/.Depend
+++ b/src/Tools/Integration/imagesView/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/imagesView.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/imagesView.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,21 +47,39 @@ imagesView.o: imagesView.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
@@ -56,26 +89,48 @@ imagesView.o: imagesView.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
+  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/blt.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltVector.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltHash.h \
-  /usr/include/inttypes.h /usr/include/stdint.h \
+  /usr/include/inttypes.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltPool.h \
   ../inc/config.h ../inc/../inc/imagesView.h \
   /Applications/Eos.app/Eos/include/tkImgFmtMRC.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
   /Applications/Eos.app/Eos/include/tkctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -83,27 +138,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/imagesView.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/imagesView.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -112,32 +182,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/imagesView.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/imagesView.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/imagesView.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/imagesView.h

diff --git a/src/Tools/Integration/imagesView/src/X86MAC64/Makefile b/src/Tools/Integration/imagesView/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/imagesView/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/imagesView/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/imagesView/src/X86MAC64/imagesView b/src/Tools/Integration/imagesView/src/X86MAC64/imagesView
index 308c175..a0f7ef9 100755 (executable)
Binary files a/src/Tools/Integration/imagesView/src/X86MAC64/imagesView and b/src/Tools/Integration/imagesView/src/X86MAC64/imagesView differ

diff --git a/src/Tools/Integration/obj3Don2DImageView/src/X86MAC64/Makefile b/src/Tools/Integration/obj3Don2DImageView/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/obj3Don2DImageView/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/obj3Don2DImageView/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/Integration/smolet/src/X86MAC64/Makefile b/src/Tools/Integration/smolet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/Integration/smolet/src/X86MAC64/Makefile
+++ b/src/Tools/Integration/smolet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/admin/mallocCheck/src/X86MAC64/Makefile b/src/Tools/admin/mallocCheck/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/admin/mallocCheck/src/X86MAC64/Makefile
+++ b/src/Tools/admin/mallocCheck/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/.Depend
index 2bcce18..40c04e2 100644 (file)
--- a/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromMultiImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromMultiImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -34,20 +48,38 @@ ctfDeterminationFromMultiImage.o: ctfDeterminationFromMultiImage.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromMultiImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromMultiImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -55,28 +87,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromMultiImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromMultiImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -85,34 +131,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromMultiImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromMultiImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromMultiImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromMultiImage.h

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/ctfDeterminationFromMultiImage b/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/ctfDeterminationFromMultiImage
index b93d710..906fb1e 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/ctfDeterminationFromMultiImage and b/src/Tools/ctfInfo/ctfDeterminationFromMultiImage/src/X86MAC64/ctfDeterminationFromMultiImage differ

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/.Depend
index 6047bc6..3aaa86e 100644 (file)
--- a/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/.Depend
@@ -3,87 +3,130 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromPhaseComparison.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromPhaseComparison.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-ctfDeterminationFromPhaseComparison.o:  \
- ctfDeterminationFromPhaseComparison.c /usr/include/stdio.h \
+ctfDeterminationFromPhaseComparison.o: \
+  ctfDeterminationFromPhaseComparison.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromPhaseComparison.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromPhaseComparison.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/ctfDeterminationFromPhaseComparison.h
+  /Applications/Eos.app/Eos/include/Array.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromPhaseComparison.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromPhaseComparison.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -92,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromPhaseComparison.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromPhaseComparison.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromPhaseComparison.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromPhaseComparison.h

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/.Depend
index 6cb71b5..a24dee0 100644 (file)
--- a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromThonRing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromThonRing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -34,63 +48,90 @@ ctfDeterminationFromThonRing.o: ctfDeterminationFromThonRing.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromThonRing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromThonRing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
+  /Applications/Eos.app/Eos/include/Array.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromThonRing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromThonRing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -99,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromThonRing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromThonRing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfDeterminationFromThonRing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDeterminationFromThonRing.h

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/ctfDeterminationFromThonRing b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/ctfDeterminationFromThonRing
index 34524ad..ddeb30c 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/ctfDeterminationFromThonRing and b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86MAC64/ctfDeterminationFromThonRing differ

diff --git a/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/.Depend
index 2b6849f..90ff9a9 100644 (file)
--- a/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfDetermine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDetermine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,41 +47,52 @@ ctfDetermine.o: ctfDetermine.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfDetermine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDetermine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lctfDetermination.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/powerspectraTangentLine.h \
-  /Applications/Eos.app/Eos/include/lctfDetermination.h \
   /Applications/Eos.app/Eos/include/lmrcFSInfoScatteringAngularDistributionAverageSection.h \
   /Applications/Eos.app/Eos/include/lastigmatismDetection.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/ctfInfoWrite2.h \
   /Applications/Eos.app/Eos/include/nr2.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -75,27 +101,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfDetermine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfDetermine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -104,32 +145,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfDetermine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDetermine.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfDetermine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfDetermine.h

diff --git a/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/ctfDetermine b/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/ctfDetermine
index 2bfdcb5..93b6cd3 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/ctfDetermine and b/src/Tools/ctfInfo/ctfDetermine/src/X86MAC64/ctfDetermine differ

diff --git a/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/.Depend
index ed9d333..0947244 100644 (file)
--- a/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ ctfEnvelopFunction.o: ctfEnvelopFunction.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfEnvelopFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfEnvelopFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfEnvelopFunction.h

diff --git a/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/ctfEnvelopFunction b/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/ctfEnvelopFunction
index cd27313..2f56490 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/ctfEnvelopFunction and b/src/Tools/ctfInfo/ctfEnvelopFunction/src/X86MAC64/ctfEnvelopFunction differ

diff --git a/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/.Depend
index e4b0e63..d967220 100644 (file)
--- a/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,61 +47,90 @@ ctfFunction.o: ctfFunction.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
+  /Applications/Eos.app/Eos/include/Array.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -95,32 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfFunction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfFunction.h

diff --git a/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/ctfFunction b/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/ctfFunction
index 14a7aaa..1821779 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/ctfFunction and b/src/Tools/ctfInfo/ctfFunction/src/X86MAC64/ctfFunction differ

diff --git a/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/.Depend
index 8596ceb..53b3ca0 100644 (file)
--- a/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfFunctionServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfFunctionServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ ctfFunctionServer.o: ctfFunctionServer.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfFunctionServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfFunctionServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfFunctionServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfFunctionServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfFunctionServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfFunctionServer.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfFunctionServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfFunctionServer.h

diff --git a/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfFunctionServer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/.Depend
index 6c4e63b..ade33b6 100644 (file)
--- a/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfInfoSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfInfoSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ ctfInfoSet.o: ctfInfoSet.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfInfoSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfInfoSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfInfoSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfInfoSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,32 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfInfoSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfInfoSet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfInfoSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfInfoSet.h

diff --git a/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/ctfInfoSet b/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/ctfInfoSet
index 8558b3a..90861a0 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/ctfInfoSet and b/src/Tools/ctfInfo/ctfInfoSet/src/X86MAC64/ctfInfoSet differ

diff --git a/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/.Depend
index fd042f8..a07c929 100644 (file)
--- a/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfMultiFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfMultiFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,20 +47,38 @@ ctfMultiFunction.o: ctfMultiFunction.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfMultiFunction.h \
-  /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfMultiFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -53,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfMultiFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfMultiFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -82,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfMultiFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfMultiFunction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfMultiFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfMultiFunction.h

diff --git a/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/ctfMultiFunction b/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/ctfMultiFunction
index ccb008b..93024cc 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/ctfMultiFunction and b/src/Tools/ctfInfo/ctfMultiFunction/src/X86MAC64/ctfMultiFunction differ

diff --git a/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/.Depend
index 4453a38..c8b8b0a 100644 (file)
--- a/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfWeightMapCreation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfWeightMapCreation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,56 +47,85 @@ ctfWeightMapCreation.o: ctfWeightMapCreation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfWeightMapCreation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfWeightMapCreation.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
+  /Applications/Eos.app/Eos/include/Array.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ctfWeightMapCreation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfWeightMapCreation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -91,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfWeightMapCreation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfWeightMapCreation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ctfWeightMapCreation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfWeightMapCreation.h

diff --git a/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/ctfWeightMapCreation b/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/ctfWeightMapCreation
index 8778aa3..104e06c 100755 (executable)
Binary files a/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/ctfWeightMapCreation and b/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86MAC64/ctfWeightMapCreation differ

diff --git a/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/.Depend b/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/.Depend
index 298d577..89903c0 100644 (file)
--- a/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfZeroPoint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfZeroPoint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,47 +47,81 @@ ctfZeroPoint.o: ctfZeroPoint.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfZeroPoint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfZeroPoint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h ../inc/ctfZeroPoint.h
+  /Applications/Eos.app/Eos/include/ctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ctfZeroPoint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ctfZeroPoint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,32 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfZeroPoint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfZeroPoint.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ctfZeroPoint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ctfZeroPoint.h

diff --git a/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/Makefile b/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/ctfZeroPoint/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/.Depend b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/.Depend
index 9d9b7b8..8e57454 100644 (file)
--- a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/defocusDeterminationFromThonRing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/defocusDeterminationFromThonRing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -34,25 +48,41 @@ defocusDeterminationFromThonRing.o: defocusDeterminationFromThonRing.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/defocusDeterminationFromThonRing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/defocusDeterminationFromThonRing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
@@ -62,28 +92,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/defocusDeterminationFromThonRing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/defocusDeterminationFromThonRing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -92,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/defocusDeterminationFromThonRing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/defocusDeterminationFromThonRing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/defocusDeterminationFromThonRing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/defocusDeterminationFromThonRing.h

diff --git a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/Makefile b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/defocusDeterminationFromThonRing b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/defocusDeterminationFromThonRing
index d8a5fa3..3ce13bb 100755 (executable)
Binary files a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/defocusDeterminationFromThonRing and b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86MAC64/defocusDeterminationFromThonRing differ

diff --git a/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/.Depend b/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/.Depend
index 415a876..8424375 100644 (file)
--- a/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/electronWaveLength.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/electronWaveLength.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ electronWaveLength.o: electronWaveLength.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/electronWaveLength.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/electronWaveLength.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/electronWaveLength.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/electronWaveLength.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/electronWaveLength.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/electronWaveLength.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/electronWaveLength.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/electronWaveLength.h

diff --git a/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/Makefile b/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/electronWaveLength b/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/electronWaveLength
index 7e63cc6..f62d8ed 100755 (executable)
Binary files a/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/electronWaveLength and b/src/Tools/ctfInfo/electronWaveLength/src/X86MAC64/electronWaveLength differ

diff --git a/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/.Depend b/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/.Depend
index 1373713..2b29204 100644 (file)
--- a/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/molecularEnvelopeResampling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molecularEnvelopeResampling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/molecularEnvelopeResampling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molecularEnvelopeResampling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,20 +92,38 @@ molecularEnvelopeResampling.o: molecularEnvelopeResampling.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/molecularEnvelopeResampling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molecularEnvelopeResampling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -85,34 +131,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/molecularEnvelopeResampling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molecularEnvelopeResampling.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/molecularEnvelopeResampling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molecularEnvelopeResampling.h

diff --git a/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/Makefile b/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/molecularEnvelopeResampling b/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/molecularEnvelopeResampling
index f501c61..5009f2d 100755 (executable)
Binary files a/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/molecularEnvelopeResampling and b/src/Tools/ctfInfo/molecularEnvelopeResampling/src/X86MAC64/molecularEnvelopeResampling differ

diff --git a/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/.Depend b/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/.Depend
index de61f2d..6c43cad 100644 (file)
--- a/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/.Depend
+++ b/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tiltInfoDetermine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tiltInfoDetermine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tiltInfoDetermine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tiltInfoDetermine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,77 +91,126 @@ tiltInfoDetermine.o: tiltInfoDetermine.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
   ../inc/config.h ../inc/../inc/tiltInfoDetermine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/nr2.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/lmrcImageROI2D.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageMontage.h \
-  /Applications/Eos.app/Eos/include/lmrcImagePad.h \
-  /Applications/Eos.app/Eos/include/Memory.h
+  /Applications/Eos.app/Eos/include/lmrcImagePad.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/tiltInfoDetermine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/tiltInfoDetermine.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/tiltInfoDetermine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/tiltInfoDetermine.h

diff --git a/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/Makefile b/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/Makefile
+++ b/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/tiltInfoDetermine b/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/tiltInfoDetermine
index f0cb4f3..635fa89 100755 (executable)
Binary files a/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/tiltInfoDetermine and b/src/Tools/ctfInfo/tiltInfoDetermine/src/X86MAC64/tiltInfoDetermine differ

diff --git a/src/Tools/database/homology2PG/src/X86MAC64/Makefile b/src/Tools/database/homology2PG/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/database/homology2PG/src/X86MAC64/Makefile
+++ b/src/Tools/database/homology2PG/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/database/pgDataBaseSelectServer/src/X86MAC64/Makefile b/src/Tools/database/pgDataBaseSelectServer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/database/pgDataBaseSelectServer/src/X86MAC64/Makefile
+++ b/src/Tools/database/pgDataBaseSelectServer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/database/pgJournalSelect/src/X86MAC64/Makefile b/src/Tools/database/pgJournalSelect/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/database/pgJournalSelect/src/X86MAC64/Makefile
+++ b/src/Tools/database/pgJournalSelect/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/database/pgJournalSelectCORBAClient/src/X86MAC64/Makefile b/src/Tools/database/pgJournalSelectCORBAClient/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/database/pgJournalSelectCORBAClient/src/X86MAC64/Makefile
+++ b/src/Tools/database/pgJournalSelectCORBAClient/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/database/pgJournalSelectCORBAServer/src/X86MAC64/Makefile b/src/Tools/database/pgJournalSelectCORBAServer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/database/pgJournalSelectCORBAServer/src/X86MAC64/Makefile
+++ b/src/Tools/database/pgJournalSelectCORBAServer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/database/pgMemoSelectCORBAServer/src/X86MAC64/Makefile b/src/Tools/database/pgMemoSelectCORBAServer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/database/pgMemoSelectCORBAServer/src/X86MAC64/Makefile
+++ b/src/Tools/database/pgMemoSelectCORBAServer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/database/pgSelect/src/X86MAC64/Makefile b/src/Tools/database/pgSelect/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/database/pgSelect/src/X86MAC64/Makefile
+++ b/src/Tools/database/pgSelect/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/array2mrc/src/X86MAC64/.Depend b/src/Tools/filter/array2mrc/src/X86MAC64/.Depend
index cda235e..5560f2c 100644 (file)
--- a/src/Tools/filter/array2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/filter/array2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/array2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/array2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,55 +47,86 @@ array2mrc.o: array2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/array2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/array2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/larray2mrc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/larray2mrc.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/array2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/array2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -89,32 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/array2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/array2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/array2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/array2mrc.h

diff --git a/src/Tools/filter/array2mrc/src/X86MAC64/Makefile b/src/Tools/filter/array2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/array2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/filter/array2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/array2mrc/src/X86MAC64/array2mrc b/src/Tools/filter/array2mrc/src/X86MAC64/array2mrc
index 3d8c834..f48a2e3 100755 (executable)
Binary files a/src/Tools/filter/array2mrc/src/X86MAC64/array2mrc and b/src/Tools/filter/array2mrc/src/X86MAC64/array2mrc differ

diff --git a/src/Tools/filter/bin2mrc/src/X86MAC64/.Depend b/src/Tools/filter/bin2mrc/src/X86MAC64/.Depend
index 133eff4..14e1977 100644 (file)
--- a/src/Tools/filter/bin2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/filter/bin2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/bin2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/bin2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,30 +47,45 @@ bin2mrc.o: bin2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/bin2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/bin2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -65,27 +95,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/bin2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/bin2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -94,32 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/bin2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/bin2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/bin2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/bin2mrc.h

diff --git a/src/Tools/filter/bin2mrc/src/X86MAC64/Makefile b/src/Tools/filter/bin2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/bin2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/filter/bin2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/bin2mrc/src/X86MAC64/bin2mrc b/src/Tools/filter/bin2mrc/src/X86MAC64/bin2mrc
index 2e778d1..8db3c33 100755 (executable)
Binary files a/src/Tools/filter/bin2mrc/src/X86MAC64/bin2mrc and b/src/Tools/filter/bin2mrc/src/X86MAC64/bin2mrc differ

diff --git a/src/Tools/filter/dos2unix/src/X86MAC64/.Depend b/src/Tools/filter/dos2unix/src/X86MAC64/.Depend
index 607e4f6..a4ace94 100644 (file)
--- a/src/Tools/filter/dos2unix/src/X86MAC64/.Depend
+++ b/src/Tools/filter/dos2unix/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dos2unix.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dos2unix.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,46 +47,80 @@ dos2unix.o: dos2unix.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dos2unix.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dos2unix.h \
   /Applications/Eos.app/Eos/include/genUtil.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/dos2unix.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/dos2unix.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -80,32 +129,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/dos2unix.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/dos2unix.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/dos2unix.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/dos2unix.h

diff --git a/src/Tools/filter/dos2unix/src/X86MAC64/Makefile b/src/Tools/filter/dos2unix/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/dos2unix/src/X86MAC64/Makefile
+++ b/src/Tools/filter/dos2unix/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/dos2unix/src/X86MAC64/dos2unix b/src/Tools/filter/dos2unix/src/X86MAC64/dos2unix
index 4da5ce8..fc75fe9 100755 (executable)
Binary files a/src/Tools/filter/dos2unix/src/X86MAC64/dos2unix and b/src/Tools/filter/dos2unix/src/X86MAC64/dos2unix differ

diff --git a/src/Tools/filter/emData2mrc/src/X86MAC64/.Depend b/src/Tools/filter/emData2mrc/src/X86MAC64/.Depend
index 42b1b70..eceeb47 100644 (file)
--- a/src/Tools/filter/emData2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/filter/emData2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/emData2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/emData2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,22 +47,40 @@ emData2mrc.o: emData2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/emData2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/emData2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -58,27 +91,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/emData2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/emData2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -87,32 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/emData2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/emData2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/emData2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/emData2mrc.h

diff --git a/src/Tools/filter/emData2mrc/src/X86MAC64/Makefile b/src/Tools/filter/emData2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/emData2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/filter/emData2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/emData2mrc/src/X86MAC64/emData2mrc b/src/Tools/filter/emData2mrc/src/X86MAC64/emData2mrc
index 6c5fbaf..9a860c8 100755 (executable)
Binary files a/src/Tools/filter/emData2mrc/src/X86MAC64/emData2mrc and b/src/Tools/filter/emData2mrc/src/X86MAC64/emData2mrc differ

diff --git a/src/Tools/filter/imodst2mrc/src/X86MAC64/.Depend b/src/Tools/filter/imodst2mrc/src/X86MAC64/.Depend
index bb4175d..485a127 100644 (file)
--- a/src/Tools/filter/imodst2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/filter/imodst2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/imodst2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/imodst2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,22 +47,40 @@ imodst2mrc.o: imodst2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/imodst2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/imodst2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -57,27 +90,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/imodst2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/imodst2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -86,32 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/imodst2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/imodst2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/imodst2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/imodst2mrc.h

diff --git a/src/Tools/filter/imodst2mrc/src/X86MAC64/Makefile b/src/Tools/filter/imodst2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/imodst2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/filter/imodst2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/imodst2mrc/src/X86MAC64/imodst2mrc b/src/Tools/filter/imodst2mrc/src/X86MAC64/imodst2mrc
index 8788388..af3da13 100755 (executable)
Binary files a/src/Tools/filter/imodst2mrc/src/X86MAC64/imodst2mrc and b/src/Tools/filter/imodst2mrc/src/X86MAC64/imodst2mrc differ

diff --git a/src/Tools/filter/ip2mrc/src/X86MAC64/.Depend b/src/Tools/filter/ip2mrc/src/X86MAC64/.Depend
index b7899a2..61388a1 100644 (file)
--- a/src/Tools/filter/ip2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/filter/ip2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ip2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ip2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ip2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ip2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,30 +91,45 @@ ip2mrc.o: ip2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ip2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ip2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -94,32 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ip2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ip2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ip2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ip2mrc.h

diff --git a/src/Tools/filter/ip2mrc/src/X86MAC64/Makefile b/src/Tools/filter/ip2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/ip2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/filter/ip2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/ip2mrc/src/X86MAC64/ip2mrc b/src/Tools/filter/ip2mrc/src/X86MAC64/ip2mrc
index fc7a111..baf894c 100755 (executable)
Binary files a/src/Tools/filter/ip2mrc/src/X86MAC64/ip2mrc and b/src/Tools/filter/ip2mrc/src/X86MAC64/ip2mrc differ

diff --git a/src/Tools/filter/moi2mrc/src/X86MAC64/.Depend b/src/Tools/filter/moi2mrc/src/X86MAC64/.Depend
index 6bb0a74..eb862b4 100644 (file)
--- a/src/Tools/filter/moi2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/filter/moi2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/moi2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/moi2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/moi2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/moi2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,31 +91,45 @@ moi2mrc.o: moi2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/moi2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/moi2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -95,32 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/moi2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/moi2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/moi2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/moi2mrc.h

diff --git a/src/Tools/filter/moi2mrc/src/X86MAC64/Makefile b/src/Tools/filter/moi2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/moi2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/filter/moi2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/moi2mrc/src/X86MAC64/moi2mrc b/src/Tools/filter/moi2mrc/src/X86MAC64/moi2mrc
index 0b48ee9..db7952c 100755 (executable)
Binary files a/src/Tools/filter/moi2mrc/src/X86MAC64/moi2mrc and b/src/Tools/filter/moi2mrc/src/X86MAC64/moi2mrc differ

diff --git a/src/Tools/filter/mrc2fld/src/X86MAC64/.Depend b/src/Tools/filter/mrc2fld/src/X86MAC64/.Depend
index 68d6ac3..7b50355 100644 (file)
--- a/src/Tools/filter/mrc2fld/src/X86MAC64/.Depend
+++ b/src/Tools/filter/mrc2fld/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2fld.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2fld.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2fld.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2fld.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,58 +93,112 @@ mrc2fld.o: mrc2fld.c /Applications/Eos.app/Eos/include/genUtil.h \
   /usr/include/AvailabilityInternal.h /usr/include/stdio.h \
   /usr/include/_types.h /usr/include/sys/_types.h \
   /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
+  /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h \
+  /usr/include/sys/_types/_null.h /usr/include/sys/_types/_off_t.h \
+  /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \
+  /usr/include/secure/_common.h /usr/include/stdlib.h \
+  /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h \
+  /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h \
   /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/signal.h /usr/include/machine/_mcontext.h \
+  /usr/include/i386/_mcontext.h /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  ../inc/config.h ../inc/../inc/mrc2fld.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h ../inc/config.h \
+  ../inc/../inc/mrc2fld.h /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/avsFile.h \
-  /Applications/Eos.app/Eos/include/lmrcImageModeChange.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageModeChange.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2fld.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2fld.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2fld.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2fld.h

diff --git a/src/Tools/filter/mrc2fld/src/X86MAC64/Makefile b/src/Tools/filter/mrc2fld/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/mrc2fld/src/X86MAC64/Makefile
+++ b/src/Tools/filter/mrc2fld/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/mrc2fld/src/X86MAC64/mrc2fld b/src/Tools/filter/mrc2fld/src/X86MAC64/mrc2fld
index 8206d1a..3f18cd8 100755 (executable)
Binary files a/src/Tools/filter/mrc2fld/src/X86MAC64/mrc2fld and b/src/Tools/filter/mrc2fld/src/X86MAC64/mrc2fld differ

diff --git a/src/Tools/filter/mrc2gif/src/X86MAC64/.Depend b/src/Tools/filter/mrc2gif/src/X86MAC64/.Depend
index f3d8f45..93d965a 100644 (file)
--- a/src/Tools/filter/mrc2gif/src/X86MAC64/.Depend
+++ b/src/Tools/filter/mrc2gif/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2gif.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2gif.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2gif.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2gif.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrc2gif.o: mrc2gif.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2gif.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2gif.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -81,39 +130,76 @@ mrc2gif.o: mrc2gif.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/gifFile.h \
-  /Applications/Eos.app/Eos/include/gif_lib.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/gif_lib.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2gif.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2gif.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2gif.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2gif.h

diff --git a/src/Tools/filter/mrc2gif/src/X86MAC64/Makefile b/src/Tools/filter/mrc2gif/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/mrc2gif/src/X86MAC64/Makefile
+++ b/src/Tools/filter/mrc2gif/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/mrc2gif/src/X86MAC64/mrc2gif b/src/Tools/filter/mrc2gif/src/X86MAC64/mrc2gif
index f8b46e1..132c029 100755 (executable)
Binary files a/src/Tools/filter/mrc2gif/src/X86MAC64/mrc2gif and b/src/Tools/filter/mrc2gif/src/X86MAC64/mrc2gif differ

diff --git a/src/Tools/filter/mrc2lattice/src/X86MAC64/.Depend b/src/Tools/filter/mrc2lattice/src/X86MAC64/.Depend
index 4a02a10..67865e9 100644 (file)
--- a/src/Tools/filter/mrc2lattice/src/X86MAC64/.Depend
+++ b/src/Tools/filter/mrc2lattice/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2lattice.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2lattice.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2lattice.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2lattice.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,31 +91,46 @@ mrc2lattice.o: mrc2lattice.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2lattice.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2lattice.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -94,32 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2lattice.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2lattice.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2lattice.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2lattice.h

diff --git a/src/Tools/filter/mrc2lattice/src/X86MAC64/Makefile b/src/Tools/filter/mrc2lattice/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/mrc2lattice/src/X86MAC64/Makefile
+++ b/src/Tools/filter/mrc2lattice/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/mrc2mrc/src/X86MAC64/.Depend b/src/Tools/filter/mrc2mrc/src/X86MAC64/.Depend
new file mode 100644 (file)
index 0000000..ea74fff
--- /dev/null
+++ b/src/Tools/filter/mrc2mrc/src/X86MAC64/.Depend
@@ -0,0 +1,203 @@
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2mrc.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
+  /usr/include/limits.h /usr/include/machine/limits.h \
+  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
+  /usr/include/sys/syslimits.h
+init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2mrc.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
+  /usr/include/limits.h /usr/include/machine/limits.h \
+  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
+  /usr/include/sys/syslimits.h
+mrc2mrc.o: mrc2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2mrc.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Array.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2mrc.h
+util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2mrc.h

diff --git a/src/Tools/filter/mrc2mrc/src/X86MAC64/Makefile b/src/Tools/filter/mrc2mrc/src/X86MAC64/Makefile
new file mode 100755 (executable)
index 0000000..ec61247
--- /dev/null
+++ b/src/Tools/filter/mrc2mrc/src/X86MAC64/Makefile
@@ -0,0 +1,114 @@
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineTool.inc
+
+LIBFILES   = \
+                       $(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+                       $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+                       $(OBJECTNAME).c \
+                       init.c \
+                       argCheck.c \
+                       usage.c  \
+                       util.c 
+
+SRCCXX  = \
+                       $(OBJECTNAME).cc \
+                       init.cc \
+                       argCheck.cc \
+                       usage.cc  \
+                       util.cc 
+
+MODULES    = \
+                       $(OBJECTNAME).o \
+                       init.o \
+                       argCheck.o \
+                       usage.o  \
+                       util.o 
+
+REALMODULES    = \
+                       $(OSTYPE)/$(OBJECTNAME).o \
+                       $(OSTYPE)/init.o \
+                       $(OSTYPE)/argCheck.o \
+                       $(OSTYPE)/usage.o \
+                       $(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+                       $(OBJECTNAME).debugo \
+                       init.debugo \
+                       argCheck.debugo \
+                       usage.debugo  \
+                       util.debugo 
+
+MODULESCUDAGDB    = \
+                       $(OBJECTNAME).cudagdb.o \
+                       init.cudagdb.o \
+                       argCheck.cudagdb.o \
+                       usage.cudagdb.o  \
+                       util.cudagdb.o 
+
+REALMODULESDEBUG    = \
+                       $(OSTYPE)/$(OBJECTNAME).debugo \
+                       $(OSTYPE)/init.debugo \
+                       $(OSTYPE)/argCheck.debugo \
+                       $(OSTYPE)/usage.debugo \
+                       $(OSTYPE)/util.debugo 
+
+
+$(OBJECTNAME): $(MODULES) $(LIBFILES)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+       fi
+
+
+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+
+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
+       echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
+       $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
+
+include ./.Depend
+include  $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc

diff --git a/src/Tools/filter/mrc2mrc/src/X86MAC64/X86MAC64 b/src/Tools/filter/mrc2mrc/src/X86MAC64/X86MAC64
new file mode 120000 (symlink)
index 0000000..0334e60
--- /dev/null
+++ b/src/Tools/filter/mrc2mrc/src/X86MAC64/X86MAC64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86MAC64/src/Tools/filter/mrc2mrc/src/X86MAC64
\ No newline at end of file

diff --git a/src/Tools/filter/mrc2mrc/src/X86MAC64/mrc2mrc b/src/Tools/filter/mrc2mrc/src/X86MAC64/mrc2mrc
new file mode 100755 (executable)
index 0000000..40b135b
Binary files /dev/null and b/src/Tools/filter/mrc2mrc/src/X86MAC64/mrc2mrc differ

diff --git a/src/Tools/filter/mrc2pov/src/X86MAC64/.Depend b/src/Tools/filter/mrc2pov/src/X86MAC64/.Depend
index 1f74b47..72b7a0b 100644 (file)
--- a/src/Tools/filter/mrc2pov/src/X86MAC64/.Depend
+++ b/src/Tools/filter/mrc2pov/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2pov.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2pov.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2pov.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2pov.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,24 +91,41 @@ mrc2pov.o: mrc2pov.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2pov.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2pov.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -88,32 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2pov.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2pov.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2pov.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2pov.h

diff --git a/src/Tools/filter/mrc2pov/src/X86MAC64/Makefile b/src/Tools/filter/mrc2pov/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/mrc2pov/src/X86MAC64/Makefile
+++ b/src/Tools/filter/mrc2pov/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/mrc2tiff/src/X86MAC64/.Depend b/src/Tools/filter/mrc2tiff/src/X86MAC64/.Depend
index e443029..1eb8229 100644 (file)
--- a/src/Tools/filter/mrc2tiff/src/X86MAC64/.Depend
+++ b/src/Tools/filter/mrc2tiff/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2tiff.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2tiff.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2tiff.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2tiff.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,24 +91,40 @@ mrc2tiff.o: mrc2tiff.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2tiff.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2tiff.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
@@ -92,38 +138,76 @@ mrc2tiff.o: mrc2tiff.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tiff.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tiffconf.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tiffvers.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2tiff.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2tiff.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2tiff.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2tiff.h

diff --git a/src/Tools/filter/mrc2tiff/src/X86MAC64/Makefile b/src/Tools/filter/mrc2tiff/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/mrc2tiff/src/X86MAC64/Makefile
+++ b/src/Tools/filter/mrc2tiff/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/mrc2tiff/src/X86MAC64/mrc2tiff b/src/Tools/filter/mrc2tiff/src/X86MAC64/mrc2tiff
index acad3e3..86ac283 100755 (executable)
Binary files a/src/Tools/filter/mrc2tiff/src/X86MAC64/mrc2tiff and b/src/Tools/filter/mrc2tiff/src/X86MAC64/mrc2tiff differ

diff --git a/src/Tools/filter/mrc2viff/src/X86MAC64/.Depend b/src/Tools/filter/mrc2viff/src/X86MAC64/.Depend
index 8c2f962..5b1aea6 100644 (file)
--- a/src/Tools/filter/mrc2viff/src/X86MAC64/.Depend
+++ b/src/Tools/filter/mrc2viff/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2viff.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2viff.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2viff.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2viff.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,32 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2viff.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2viff.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2viff.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2viff.h

diff --git a/src/Tools/filter/mrc2viff/src/X86MAC64/Makefile b/src/Tools/filter/mrc2viff/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/mrc2viff/src/X86MAC64/Makefile
+++ b/src/Tools/filter/mrc2viff/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/pdb2ucd/src/X86MAC64/.Depend b/src/Tools/filter/pdb2ucd/src/X86MAC64/.Depend
index 7fbf486..5d6c8a2 100644 (file)
--- a/src/Tools/filter/pdb2ucd/src/X86MAC64/.Depend
+++ b/src/Tools/filter/pdb2ucd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2ucd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2ucd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2ucd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2ucd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,26 +91,44 @@ pdb2ucd.o: pdb2ucd.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2ucd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2ucd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/avsFile.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -88,32 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2ucd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2ucd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2ucd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2ucd.h

diff --git a/src/Tools/filter/pdb2ucd/src/X86MAC64/Makefile b/src/Tools/filter/pdb2ucd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/pdb2ucd/src/X86MAC64/Makefile
+++ b/src/Tools/filter/pdb2ucd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/pdb2ucd/src/X86MAC64/pdb2ucd b/src/Tools/filter/pdb2ucd/src/X86MAC64/pdb2ucd
index e54c283..6f67db1 100755 (executable)
Binary files a/src/Tools/filter/pdb2ucd/src/X86MAC64/pdb2ucd and b/src/Tools/filter/pdb2ucd/src/X86MAC64/pdb2ucd differ

diff --git a/src/Tools/filter/test2/src/X86MAC64/.Depend b/src/Tools/filter/test2/src/X86MAC64/.Depend
index 0b14841..bc50cdf 100644 (file)
--- a/src/Tools/filter/test2/src/X86MAC64/.Depend
+++ b/src/Tools/filter/test2/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/test.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/test.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/test.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/test.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,32 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/test.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/test.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/test.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/test.h

diff --git a/src/Tools/filter/test2/src/X86MAC64/Makefile b/src/Tools/filter/test2/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/test2/src/X86MAC64/Makefile
+++ b/src/Tools/filter/test2/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/tgaInfo/src/X86MAC64/.Depend b/src/Tools/filter/tgaInfo/src/X86MAC64/.Depend
index f9e19a6..d774054 100644 (file)
--- a/src/Tools/filter/tgaInfo/src/X86MAC64/.Depend
+++ b/src/Tools/filter/tgaInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tgaInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tgaInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tgaInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tgaInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ tgaInfo.o: tgaInfo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tgaInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tgaInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/tgaFile.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -81,32 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/tgaInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/tgaInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/tgaInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/tgaInfo.h

diff --git a/src/Tools/filter/tgaInfo/src/X86MAC64/Makefile b/src/Tools/filter/tgaInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/tgaInfo/src/X86MAC64/Makefile
+++ b/src/Tools/filter/tgaInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/tgaInfo/src/X86MAC64/tgaInfo b/src/Tools/filter/tgaInfo/src/X86MAC64/tgaInfo
index c3896d4..b719d21 100755 (executable)
Binary files a/src/Tools/filter/tgaInfo/src/X86MAC64/tgaInfo and b/src/Tools/filter/tgaInfo/src/X86MAC64/tgaInfo differ

diff --git a/src/Tools/filter/tiff2mrc/src/X86MAC64/.Depend b/src/Tools/filter/tiff2mrc/src/X86MAC64/.Depend
index ac1d1ef..c0a389d 100644 (file)
--- a/src/Tools/filter/tiff2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/filter/tiff2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tiff2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tiff2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tiff2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tiff2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,32 +91,46 @@ tiff2mrc.o: tiff2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/tiff2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/tiff2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -94,40 +138,77 @@ tiff2mrc.o: tiff2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tiff.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tiffconf.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tiffio.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tiff.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tiffvers.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/tiff2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/tiff2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/tiff2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/tiff2mrc.h

diff --git a/src/Tools/filter/tiff2mrc/src/X86MAC64/Makefile b/src/Tools/filter/tiff2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/filter/tiff2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/filter/tiff2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/filter/tiff2mrc/src/X86MAC64/tiff2mrc b/src/Tools/filter/tiff2mrc/src/X86MAC64/tiff2mrc
index f0419bb..c134544 100755 (executable)
Binary files a/src/Tools/filter/tiff2mrc/src/X86MAC64/tiff2mrc and b/src/Tools/filter/tiff2mrc/src/X86MAC64/tiff2mrc differ

diff --git a/src/Tools/hf2000/hf2000Init/src/X86MAC64/.Depend b/src/Tools/hf2000/hf2000Init/src/X86MAC64/.Depend
index 410b103..7c616ef 100644 (file)
--- a/src/Tools/hf2000/hf2000Init/src/X86MAC64/.Depend
+++ b/src/Tools/hf2000/hf2000Init/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/hf2000Init.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/hf2000Init.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,73 +47,137 @@ hf2000Init.o: hf2000Init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/unistd.h \
-  /usr/include/sys/unistd.h /usr/include/sys/select.h \
-  /usr/include/sys/_select.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/hf2000Init.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/unistd.h /usr/include/sys/unistd.h \
+  /usr/include/sys/_types/_posix_vdisable.h \
+  /usr/include/sys/_types/_seek_set.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_useconds_t.h /usr/include/sys/select.h \
+  /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_isset.h /usr/include/sys/_types/_fd_zero.h \
+  /usr/include/sys/_types/_fd_copy.h /usr/include/sys/_select.h \
+  /usr/include/sys/_types/_uuid_t.h /usr/include/gethostuuid.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/hf2000Init.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Socket.h /usr/include/sys/types.h \
-  /usr/include/sys/socket.h /usr/include/machine/_param.h \
-  /usr/include/i386/_param.h /usr/include/netinet/in.h \
-  /usr/include/stdint.h /usr/include/netinet6/in6.h /usr/include/netdb.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/sys/socket.h \
+  /usr/include/machine/_param.h /usr/include/i386/_param.h \
+  /usr/include/sys/_types/_sa_family_t.h \
+  /usr/include/sys/_types/_socklen_t.h \
+  /usr/include/sys/_types/_iovec_t.h /usr/include/netinet/in.h \
+  /usr/include/netinet6/in6.h /usr/include/netdb.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/hf2000.h \
-  /usr/include/sys/stat.h /usr/include/fcntl.h /usr/include/sys/fcntl.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/hf2000.h /usr/include/sys/stat.h \
+  /usr/include/sys/_types/_s_ifmt.h /usr/include/sys/_types/_filesec_t.h \
+  /usr/include/fcntl.h /usr/include/sys/fcntl.h \
+  /usr/include/sys/_types/_o_sync.h /usr/include/sys/_types/_o_dsync.h \
   /usr/include/termios.h /usr/include/sys/termios.h \
   /usr/include/sys/ttycom.h /usr/include/sys/ioccom.h \
   /usr/include/sys/ttydefaults.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
   /usr/include/X11/Xlib.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/hf2000Init.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/hf2000Init.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -107,32 +186,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/hf2000Init.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/hf2000Init.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/hf2000Init.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/hf2000Init.h

diff --git a/src/Tools/hf2000/hf2000Init/src/X86MAC64/Makefile b/src/Tools/hf2000/hf2000Init/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/hf2000/hf2000Init/src/X86MAC64/Makefile
+++ b/src/Tools/hf2000/hf2000Init/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/.Depend b/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/.Depend
index 0cb9941..f3605ee 100644 (file)
--- a/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/.Depend
+++ b/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/hf2000LenzCurrent.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/hf2000LenzCurrent.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,62 +47,124 @@ hf2000LenzCurrent.o: hf2000LenzCurrent.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
+  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
   ../inc/config.h ../inc/../inc/hf2000LenzCurrent.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/hf2000.h /usr/include/sys/stat.h \
-  /usr/include/fcntl.h /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_s_ifmt.h \
+  /usr/include/sys/_types/_filesec_t.h /usr/include/fcntl.h \
+  /usr/include/sys/fcntl.h /usr/include/sys/_types/_o_sync.h \
+  /usr/include/sys/_types/_o_dsync.h /usr/include/sys/_types/_seek_set.h \
+  /usr/include/termios.h /usr/include/sys/termios.h \
+  /usr/include/sys/_types/_posix_vdisable.h /usr/include/sys/ttycom.h \
   /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /Applications/Eos.app/Eos/include/lhf2000LenzCurrent.h \
-  /Applications/Eos.app/Eos/include/hf2000.h
+  /Applications/Eos.app/Eos/include/lhf2000LenzCurrent.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/hf2000LenzCurrent.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/hf2000LenzCurrent.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -96,34 +173,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/hf2000LenzCurrent.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/hf2000LenzCurrent.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/hf2000LenzCurrent.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/hf2000LenzCurrent.h

diff --git a/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/Makefile b/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/Makefile
+++ b/src/Tools/hf2000/hf2000LenzCurrent/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/.Depend b/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/.Depend
index 066e9dc..8f7b540 100644 (file)
--- a/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/.Depend
+++ b/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/hf2000SpecimenPosition.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/hf2000SpecimenPosition.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,68 +47,129 @@ hf2000SpecimenPosition.o: hf2000SpecimenPosition.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
+  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/blt.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltVector.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltHash.h \
-  /usr/include/inttypes.h /usr/include/stdint.h \
+  /usr/include/inttypes.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltPool.h \
   ../inc/config.h ../inc/../inc/hf2000SpecimenPosition.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/hf2000.h /usr/include/sys/stat.h \
-  /usr/include/fcntl.h /usr/include/sys/fcntl.h /usr/include/termios.h \
-  /usr/include/sys/termios.h /usr/include/sys/ttycom.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_s_ifmt.h \
+  /usr/include/sys/_types/_filesec_t.h /usr/include/fcntl.h \
+  /usr/include/sys/fcntl.h /usr/include/sys/_types/_o_sync.h \
+  /usr/include/sys/_types/_o_dsync.h /usr/include/sys/_types/_seek_set.h \
+  /usr/include/termios.h /usr/include/sys/termios.h \
+  /usr/include/sys/_types/_posix_vdisable.h /usr/include/sys/ttycom.h \
   /usr/include/sys/ioccom.h /usr/include/sys/ttydefaults.h \
-  /Applications/Eos.app/Eos/include/lhf2000SpecimenPosition.h \
-  /Applications/Eos.app/Eos/include/hf2000.h
+  /Applications/Eos.app/Eos/include/lhf2000SpecimenPosition.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/hf2000SpecimenPosition.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/hf2000SpecimenPosition.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -103,34 +178,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/hf2000SpecimenPosition.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/hf2000SpecimenPosition.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/hf2000SpecimenPosition.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/hf2000SpecimenPosition.h

diff --git a/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/Makefile b/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/Makefile
+++ b/src/Tools/hf2000/hf2000SpecimenPosition/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/.Depend b/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/.Depend
index d0ee575..f4d8f02 100644 (file)
--- a/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/.Depend
+++ b/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/khorosFilterGenerate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/khorosFilterGenerate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/khorosFilterGenerate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/khorosFilterGenerate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/khorosFilterGenerate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/khorosFilterGenerate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/khorosFilterGenerate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/khorosFilterGenerate.h

diff --git a/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/Makefile b/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/Makefile
+++ b/src/Tools/khorosTool/khorosFilterGenerate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/largeIP/largeIPInfo/src/X86MAC64/.Depend b/src/Tools/largeIP/largeIPInfo/src/X86MAC64/.Depend
index 856bcac..6e5dc2a 100644 (file)
--- a/src/Tools/largeIP/largeIPInfo/src/X86MAC64/.Depend
+++ b/src/Tools/largeIP/largeIPInfo/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/largeIPInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/largeIPInfo.h \
   /Applications/Eos.app/Eos/include/largeIP.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +48,43 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/largeIPInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/largeIPInfo.h \
   /Applications/Eos.app/Eos/include/largeIP.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,54 +93,110 @@ largeIPInfo.o: largeIPInfo.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/largeIP.h \
-  ../inc/config.h ../inc/../inc/largeIPInfo.h \
-  /Applications/Eos.app/Eos/include/largeIP.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/largeIP.h ../inc/config.h \
+  ../inc/../inc/largeIPInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/largeIPInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/largeIPInfo.h \
   /Applications/Eos.app/Eos/include/largeIP.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/largeIPInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/largeIPInfo.h \
   /Applications/Eos.app/Eos/include/largeIP.h

diff --git a/src/Tools/largeIP/largeIPInfo/src/X86MAC64/Makefile b/src/Tools/largeIP/largeIPInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/largeIP/largeIPInfo/src/X86MAC64/Makefile
+++ b/src/Tools/largeIP/largeIPInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/largeIP/largeIPInfo/src/X86MAC64/largeIPInfo b/src/Tools/largeIP/largeIPInfo/src/X86MAC64/largeIPInfo
index a04f26c..9f596f4 100755 (executable)
Binary files a/src/Tools/largeIP/largeIPInfo/src/X86MAC64/largeIPInfo and b/src/Tools/largeIP/largeIPInfo/src/X86MAC64/largeIPInfo differ

diff --git a/src/Tools/llData/llDataAverage/src/X86MAC64/.Depend b/src/Tools/llData/llDataAverage/src/X86MAC64/.Depend
index 7ce7cd0..c731244 100644 (file)
--- a/src/Tools/llData/llDataAverage/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataAverage/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,65 +91,117 @@ llDataAverage.o: llDataAverage.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/llData.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllDataFitAndAverage.h \
-  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllDataFit.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataAverage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataAverage.h

diff --git a/src/Tools/llData/llDataAverage/src/X86MAC64/Makefile b/src/Tools/llData/llDataAverage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataAverage/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataAverage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataAverage/src/X86MAC64/llDataAverage b/src/Tools/llData/llDataAverage/src/X86MAC64/llDataAverage
index cdabaeb..b77cba7 100755 (executable)
Binary files a/src/Tools/llData/llDataAverage/src/X86MAC64/llDataAverage and b/src/Tools/llData/llDataAverage/src/X86MAC64/llDataAverage differ

diff --git a/src/Tools/llData/llDataAxisSearch/src/X86MAC64/.Depend b/src/Tools/llData/llDataAxisSearch/src/X86MAC64/.Depend
index 5ce6ab1..984b560 100644 (file)
--- a/src/Tools/llData/llDataAxisSearch/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataAxisSearch/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,113 @@ llDataAxisSearch.o: llDataAxisSearch.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllDataAxisSearch.h \
-  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllDataFit.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataAxisSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataAxisSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataAxisSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataAxisSearch.h

diff --git a/src/Tools/llData/llDataAxisSearch/src/X86MAC64/Makefile b/src/Tools/llData/llDataAxisSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataAxisSearch/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataAxisSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataAxisSearch/src/X86MAC64/llDataAxisSearch b/src/Tools/llData/llDataAxisSearch/src/X86MAC64/llDataAxisSearch
index b5f0587..594ff67 100755 (executable)
Binary files a/src/Tools/llData/llDataAxisSearch/src/X86MAC64/llDataAxisSearch and b/src/Tools/llData/llDataAxisSearch/src/X86MAC64/llDataAxisSearch differ

diff --git a/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/.Depend b/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/.Depend
index a0fc2f5..27a6dc5 100644 (file)
--- a/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataCTFCompensate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataCTFCompensate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataCTFCompensate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataCTFCompensate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,112 @@ llDataCTFCompensate.o: llDataCTFCompensate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataCTFCompensate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataCTFCompensate.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllDataCTFCompensate.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/File.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataCTFCompensate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataCTFCompensate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataCTFCompensate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataCTFCompensate.h

diff --git a/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/Makefile b/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/llDataCTFCompensate b/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/llDataCTFCompensate
index cf4fc07..7c282ac 100755 (executable)
Binary files a/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/llDataCTFCompensate and b/src/Tools/llData/llDataCTFCompensate/src/X86MAC64/llDataCTFCompensate differ

diff --git a/src/Tools/llData/llDataCompare/src/X86MAC64/.Depend b/src/Tools/llData/llDataCompare/src/X86MAC64/.Depend
index ebca68d..3e36151 100644 (file)
--- a/src/Tools/llData/llDataCompare/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataCompare/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataCompare.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataCompare.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataCompare.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataCompare.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,65 +91,116 @@ llDataCompare.o: llDataCompare.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataCompare.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataCompare.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/llData.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lllDataCompare.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/llData.h
+  /Applications/Eos.app/Eos/include/lllDataCompare.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataCompare.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataCompare.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataCompare.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataCompare.h

diff --git a/src/Tools/llData/llDataCompare/src/X86MAC64/Makefile b/src/Tools/llData/llDataCompare/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataCompare/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataCompare/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataCompare/src/X86MAC64/llDataCompare b/src/Tools/llData/llDataCompare/src/X86MAC64/llDataCompare
index d13128e..ccc758d 100755 (executable)
Binary files a/src/Tools/llData/llDataCompare/src/X86MAC64/llDataCompare and b/src/Tools/llData/llDataCompare/src/X86MAC64/llDataCompare differ

diff --git a/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/.Depend b/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/.Depend
index 4b39699..5f8c0f7 100644 (file)
--- a/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataContributionCalcDifferentN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataContributionCalcDifferentN.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataContributionCalcDifferentN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataContributionCalcDifferentN.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,59 +92,111 @@ llDataContributionCalcDifferentN.o: llDataContributionCalcDifferentN.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataContributionCalcDifferentN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataContributionCalcDifferentN.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lllDataContributionCalcDifferentN.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
+  /Applications/Eos.app/Eos/include/lllDataContributionCalcDifferentN.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataContributionCalcDifferentN.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataContributionCalcDifferentN.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataContributionCalcDifferentN.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataContributionCalcDifferentN.h

diff --git a/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/Makefile b/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/llDataContributionCalcDifferentN b/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/llDataContributionCalcDifferentN
index d495202..66ca5b5 100755 (executable)
Binary files a/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/llDataContributionCalcDifferentN and b/src/Tools/llData/llDataContributionCalcDifferentN/src/X86MAC64/llDataContributionCalcDifferentN differ

diff --git a/src/Tools/llData/llDataDump/src/X86MAC64/.Depend b/src/Tools/llData/llDataDump/src/X86MAC64/.Depend
index 4e54c41..5b0bafa 100644 (file)
--- a/src/Tools/llData/llDataDump/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataDump/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataDump.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataDump.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataDump.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataDump.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ llDataDump.o: llDataDump.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataDump.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataDump.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
@@ -82,32 +131,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llDataDump.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataDump.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llDataDump.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataDump.h

diff --git a/src/Tools/llData/llDataDump/src/X86MAC64/Makefile b/src/Tools/llData/llDataDump/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataDump/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataDump/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataDump/src/X86MAC64/llDataDump b/src/Tools/llData/llDataDump/src/X86MAC64/llDataDump
index a41f3e5..57058f0 100755 (executable)
Binary files a/src/Tools/llData/llDataDump/src/X86MAC64/llDataDump and b/src/Tools/llData/llDataDump/src/X86MAC64/llDataDump differ

diff --git a/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/.Depend b/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/.Depend
index c3a63ba..57ba083 100644 (file)
--- a/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataEquatorAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataEquatorAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataEquatorAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataEquatorAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,58 +91,111 @@ llDataEquatorAdd.o: llDataEquatorAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataEquatorAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataEquatorAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lllDataEquatorAdd.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/llData.h
+  /Applications/Eos.app/Eos/include/lllDataEquatorAdd.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataEquatorAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataEquatorAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataEquatorAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataEquatorAdd.h

diff --git a/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/Makefile b/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/llDataEquatorAdd b/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/llDataEquatorAdd
index 17ffb3c..d68404e 100755 (executable)
Binary files a/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/llDataEquatorAdd and b/src/Tools/llData/llDataEquatorAdd/src/X86MAC64/llDataEquatorAdd differ

diff --git a/src/Tools/llData/llDataExtract/src/X86MAC64/.Depend b/src/Tools/llData/llDataExtract/src/X86MAC64/.Depend
index bcf124f..6034867 100644 (file)
--- a/src/Tools/llData/llDataExtract/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataExtract/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,58 +91,111 @@ llDataExtract.o: llDataExtract.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lllDataExtract.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/llData.h
+  /Applications/Eos.app/Eos/include/lllDataExtract.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataExtract.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataExtract.h

diff --git a/src/Tools/llData/llDataExtract/src/X86MAC64/Makefile b/src/Tools/llData/llDataExtract/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataExtract/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataExtract/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataExtract/src/X86MAC64/llDataExtract b/src/Tools/llData/llDataExtract/src/X86MAC64/llDataExtract
index d70587c..6f24268 100755 (executable)
Binary files a/src/Tools/llData/llDataExtract/src/X86MAC64/llDataExtract and b/src/Tools/llData/llDataExtract/src/X86MAC64/llDataExtract differ

diff --git a/src/Tools/llData/llDataFit/src/X86MAC64/.Depend b/src/Tools/llData/llDataFit/src/X86MAC64/.Depend
index 805c422..6ec39da 100644 (file)
--- a/src/Tools/llData/llDataFit/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataFit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,50 +91,107 @@ llDataFit.o: llDataFit.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataFit.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llDataFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataFit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llDataFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataFit.h

diff --git a/src/Tools/llData/llDataFit/src/X86MAC64/Makefile b/src/Tools/llData/llDataFit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataFit/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataFit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataFit/src/X86MAC64/llDataFit b/src/Tools/llData/llDataFit/src/X86MAC64/llDataFit
index d433956..3921e2a 100755 (executable)
Binary files a/src/Tools/llData/llDataFit/src/X86MAC64/llDataFit and b/src/Tools/llData/llDataFit/src/X86MAC64/llDataFit differ

diff --git a/src/Tools/llData/llDataFitServer/src/X86MAC64/.Depend b/src/Tools/llData/llDataFitServer/src/X86MAC64/.Depend
index 2651ee2..d56a3be 100644 (file)
--- a/src/Tools/llData/llDataFitServer/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataFitServer/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataFitServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataFitServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataFitServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataFitServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,57 +91,111 @@ llDataFitServer.o: llDataFitServer.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataFitServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataFitServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lllDataFit.h \
-  /Applications/Eos.app/Eos/include/llData.h
+  /Applications/Eos.app/Eos/include/lllDataFit.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataFitServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataFitServer.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataFitServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataFitServer.h

diff --git a/src/Tools/llData/llDataFitServer/src/X86MAC64/Makefile b/src/Tools/llData/llDataFitServer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataFitServer/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataFitServer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataInfo/src/X86MAC64/.Depend b/src/Tools/llData/llDataInfo/src/X86MAC64/.Depend
index e65d81b..c38ea62 100644 (file)
--- a/src/Tools/llData/llDataInfo/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ llDataInfo.o: llDataInfo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataInfo.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -81,33 +130,71 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llDataInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  ../inc/config.h ../inc/../inc/llDataInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h ../inc/config.h \
+  ../inc/../inc/llDataInfo.h

diff --git a/src/Tools/llData/llDataInfo/src/X86MAC64/Makefile b/src/Tools/llData/llDataInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataInfo/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataInfo/src/X86MAC64/llDataInfo b/src/Tools/llData/llDataInfo/src/X86MAC64/llDataInfo
index 9ce3fd1..6c42894 100755 (executable)
Binary files a/src/Tools/llData/llDataInfo/src/X86MAC64/llDataInfo and b/src/Tools/llData/llDataInfo/src/X86MAC64/llDataInfo differ

diff --git a/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/.Depend b/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/.Depend
index 2c5a5c3..9e5e843 100644 (file)
--- a/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataLowPassFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataLowPassFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataLowPassFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataLowPassFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,59 +91,112 @@ llDataLowPassFiltering.o: llDataLowPassFiltering.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataLowPassFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataLowPassFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lllDataLowPassFiltering.h \
-  /Applications/Eos.app/Eos/include/llData.h
+  /Applications/Eos.app/Eos/include/lllDataLowPassFiltering.h
 test.o: test.c
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataLowPassFiltering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataLowPassFiltering.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataLowPassFiltering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataLowPassFiltering.h

diff --git a/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/Makefile b/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/llDataLowPassFiltering b/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/llDataLowPassFiltering
index 723f78f..f033e32 100755 (executable)
Binary files a/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/llDataLowPassFiltering and b/src/Tools/llData/llDataLowPassFiltering/src/X86MAC64/llDataLowPassFiltering differ

diff --git a/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/.Depend b/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/.Depend
index 8e9fefe..c4d5bb3 100644 (file)
--- a/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataMultiCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataMultiCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataMultiCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataMultiCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,70 +92,119 @@ llDataMultiCTFCompensation.o: llDataMultiCTFCompensation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  ../inc/config.h ../inc/../inc/llDataMultiCTFCompensation.h \
+  /usr/include/sys/syslimits.h ../inc/config.h \
+  ../inc/../inc/llDataMultiCTFCompensation.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllDataLowPassFiltering.h \
-  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllDataFitAndAverage.h \
   /Applications/Eos.app/Eos/include/lllDataFit.h \
-  /Applications/Eos.app/Eos/include/lllDataCTFCompensation.h \
-  /Applications/Eos.app/Eos/include/lllDataFitAndAverage.h
+  /Applications/Eos.app/Eos/include/lllDataCTFCompensation.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataMultiCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataMultiCTFCompensation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataMultiCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataMultiCTFCompensation.h

diff --git a/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/Makefile b/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/llDataMultiCTFCompensation b/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/llDataMultiCTFCompensation
index 2b187a3..ac58973 100755 (executable)
Binary files a/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/llDataMultiCTFCompensation and b/src/Tools/llData/llDataMultiCTFCompensation/src/X86MAC64/llDataMultiCTFCompensation differ

diff --git a/src/Tools/llData/llDataNEstimation/src/X86MAC64/.Depend b/src/Tools/llData/llDataNEstimation/src/X86MAC64/.Depend
index 4286e8d..68c78b3 100644 (file)
--- a/src/Tools/llData/llDataNEstimation/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataNEstimation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataNEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataNEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataNEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataNEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,114 @@ llDataNEstimation.o: llDataNEstimation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataNEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataNEstimation.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataNEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataNEstimation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataNEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataNEstimation.h

diff --git a/src/Tools/llData/llDataNEstimation/src/X86MAC64/Makefile b/src/Tools/llData/llDataNEstimation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataNEstimation/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataNEstimation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataNEstimation/src/X86MAC64/llDataNEstimation b/src/Tools/llData/llDataNEstimation/src/X86MAC64/llDataNEstimation
index 71973ce..39d125f 100755 (executable)
Binary files a/src/Tools/llData/llDataNEstimation/src/X86MAC64/llDataNEstimation and b/src/Tools/llData/llDataNEstimation/src/X86MAC64/llDataNEstimation differ

diff --git a/src/Tools/llData/llDataNormalization/src/X86MAC64/.Depend b/src/Tools/llData/llDataNormalization/src/X86MAC64/.Depend
index 6082741..cc7d41c 100644 (file)
--- a/src/Tools/llData/llDataNormalization/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataNormalization/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataNormalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataNormalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataNormalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataNormalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,58 +91,112 @@ llDataNormalization.o: llDataNormalization.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataNormalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataNormalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllDataDifferenceCalc.h \
-  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/Vector.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataNormalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataNormalization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataNormalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataNormalization.h

diff --git a/src/Tools/llData/llDataNormalization/src/X86MAC64/Makefile b/src/Tools/llData/llDataNormalization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataNormalization/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataNormalization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataNormalization/src/X86MAC64/llDataNormalization b/src/Tools/llData/llDataNormalization/src/X86MAC64/llDataNormalization
index 7a41daf..c2c1741 100755 (executable)
Binary files a/src/Tools/llData/llDataNormalization/src/X86MAC64/llDataNormalization and b/src/Tools/llData/llDataNormalization/src/X86MAC64/llDataNormalization differ

diff --git a/src/Tools/llData/llDataPrint/src/X86MAC64/.Depend b/src/Tools/llData/llDataPrint/src/X86MAC64/.Depend
index a90201e..ea71f31 100644 (file)
--- a/src/Tools/llData/llDataPrint/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataPrint/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataPrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataPrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataPrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataPrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,75 +91,155 @@ llDataPrint.o: llDataPrint.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/libgen.h ../inc/config.h \
-  ../inc/../inc/llDataPrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/libgen.h ../inc/config.h ../inc/../inc/llDataPrint.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
+  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/blt.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltVector.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltHash.h \
-  /usr/include/inttypes.h /usr/include/stdint.h \
+  /usr/include/inttypes.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/bltPool.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/llData.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llDataPrint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataPrint.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llDataPrint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataPrint.h

diff --git a/src/Tools/llData/llDataPrint/src/X86MAC64/Makefile b/src/Tools/llData/llDataPrint/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataPrint/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataPrint/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataPrint/src/X86MAC64/llDataPrint b/src/Tools/llData/llDataPrint/src/X86MAC64/llDataPrint
index 7eeb73b..c7fc282 100755 (executable)
Binary files a/src/Tools/llData/llDataPrint/src/X86MAC64/llDataPrint and b/src/Tools/llData/llDataPrint/src/X86MAC64/llDataPrint differ

diff --git a/src/Tools/llData/llDataRescaling/src/X86MAC64/.Depend b/src/Tools/llData/llDataRescaling/src/X86MAC64/.Depend
index 3c554d0..5e2f7b6 100644 (file)
--- a/src/Tools/llData/llDataRescaling/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataRescaling/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataRescaling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataRescaling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataRescaling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataRescaling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,57 +91,111 @@ llDataRescaling.o: llDataRescaling.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataRescaling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataRescaling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lllDataRescaling.h \
-  /Applications/Eos.app/Eos/include/llData.h
+  /Applications/Eos.app/Eos/include/lllDataRescaling.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataRescaling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataRescaling.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataRescaling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataRescaling.h

diff --git a/src/Tools/llData/llDataRescaling/src/X86MAC64/Makefile b/src/Tools/llData/llDataRescaling/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataRescaling/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataRescaling/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataRescaling/src/X86MAC64/llDataRescaling b/src/Tools/llData/llDataRescaling/src/X86MAC64/llDataRescaling
index 93062ae..5110379 100755 (executable)
Binary files a/src/Tools/llData/llDataRescaling/src/X86MAC64/llDataRescaling and b/src/Tools/llData/llDataRescaling/src/X86MAC64/llDataRescaling differ

diff --git a/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/.Depend b/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/.Depend
index be47434..ed52d95 100644 (file)
--- a/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataResolutionCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataResolutionCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataResolutionCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataResolutionCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,63 +91,115 @@ llDataResolutionCheck.o: llDataResolutionCheck.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataResolutionCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataResolutionCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/llData.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataResolutionCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataResolutionCheck.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataResolutionCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataResolutionCheck.h

diff --git a/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/Makefile b/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/llDataResolutionCheck b/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/llDataResolutionCheck
index 91b040a..2bbf381 100755 (executable)
Binary files a/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/llDataResolutionCheck and b/src/Tools/llData/llDataResolutionCheck/src/X86MAC64/llDataResolutionCheck differ

diff --git a/src/Tools/llData/llDataRotation/src/X86MAC64/.Depend b/src/Tools/llData/llDataRotation/src/X86MAC64/.Depend
index 55e3d33..fe6dde3 100644 (file)
--- a/src/Tools/llData/llDataRotation/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataRotation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ llDataRotation.o: llDataRotation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataRotation.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataRotation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataRotation.h

diff --git a/src/Tools/llData/llDataRotation/src/X86MAC64/Makefile b/src/Tools/llData/llDataRotation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataRotation/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataRotation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/.Depend b/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/.Depend
index 80965d3..1493b87 100644 (file)
--- a/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataSelectionEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataSelectionEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataSelectionEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataSelectionEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,28 +92,43 @@ llDataSelectionEstimation.o: llDataSelectionEstimation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llDataSelectionEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataSelectionEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -94,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataSelectionEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataSelectionEstimation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataSelectionEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataSelectionEstimation.h

diff --git a/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/Makefile b/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/llDataSelectionEstimation b/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/llDataSelectionEstimation
index cffe0cc..f1cc07e 100755 (executable)
Binary files a/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/llDataSelectionEstimation and b/src/Tools/llData/llDataSelectionEstimation/src/X86MAC64/llDataSelectionEstimation differ

diff --git a/src/Tools/llData/llDataSeparate/src/X86MAC64/.Depend b/src/Tools/llData/llDataSeparate/src/X86MAC64/.Depend
index 128d0ef..a46ad7d 100644 (file)
--- a/src/Tools/llData/llDataSeparate/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataSeparate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataSeparate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataSeparate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataSeparate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataSeparate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,76 +91,123 @@ llDataSeparate.o: llDataSeparate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataSeparate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataSeparate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllExtract.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllDataFit.h \
   /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h \
-  /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h \
   /Applications/Eos.app/Eos/include/lllDataLowPassFiltering.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataSeparate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataSeparate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataSeparate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataSeparate.h

diff --git a/src/Tools/llData/llDataSeparate/src/X86MAC64/Makefile b/src/Tools/llData/llDataSeparate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataSeparate/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataSeparate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataWeightSet/src/X86MAC64/.Depend b/src/Tools/llData/llDataWeightSet/src/X86MAC64/.Depend
index 0770421..83a0760 100644 (file)
--- a/src/Tools/llData/llDataWeightSet/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDataWeightSet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataWeightSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataWeightSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataWeightSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataWeightSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ llDataWeightSet.o: llDataWeightSet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDataWeightSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDataWeightSet.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataWeightSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataWeightSet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDataWeightSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDataWeightSet.h

diff --git a/src/Tools/llData/llDataWeightSet/src/X86MAC64/Makefile b/src/Tools/llData/llDataWeightSet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDataWeightSet/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDataWeightSet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDataWeightSet/src/X86MAC64/llDataWeightSet b/src/Tools/llData/llDataWeightSet/src/X86MAC64/llDataWeightSet
index 0b7f76e..53a811f 100755 (executable)
Binary files a/src/Tools/llData/llDataWeightSet/src/X86MAC64/llDataWeightSet and b/src/Tools/llData/llDataWeightSet/src/X86MAC64/llDataWeightSet differ

diff --git a/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/.Depend b/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/.Depend
index 18bfeb3..5932902 100644 (file)
--- a/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/.Depend
+++ b/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDatarMaxLimit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDatarMaxLimit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDatarMaxLimit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDatarMaxLimit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,58 +91,111 @@ llDatarMaxLimit.o: llDatarMaxLimit.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llDatarMaxLimit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llDatarMaxLimit.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/genUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDatarMaxLimit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDatarMaxLimit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llDatarMaxLimit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llDatarMaxLimit.h

diff --git a/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/Makefile b/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/Makefile
+++ b/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/llDatarMaxLimit b/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/llDatarMaxLimit
index 6c7f46d..abd8b00 100755 (executable)
Binary files a/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/llDatarMaxLimit and b/src/Tools/llData/llDatarMaxLimit/src/X86MAC64/llDatarMaxLimit differ

diff --git a/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/.Depend b/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/.Depend
index 1021664..d7a31f6 100644 (file)
--- a/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/.Depend
+++ b/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlgDataInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlgDataInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlgDataInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlgDataInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,51 +91,108 @@ ltlgDataInfo.o: ltlgDataInfo.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlgDataInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlgDataInfo.h \
   /Applications/Eos.app/Eos/include/ltlgData.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ltlgDataInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ltlgDataInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ltlgDataInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ltlgDataInfo.h

diff --git a/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/Makefile b/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/Makefile
+++ b/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/ltlgDataInfo b/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/ltlgDataInfo
index 427ab55..d0274f1 100755 (executable)
Binary files a/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/ltlgDataInfo and b/src/Tools/ltlgData/ltlgDataInfo/src/X86MAC64/ltlgDataInfo differ

diff --git a/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/.Depend b/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/.Depend
index 0331166..eb62cea 100644 (file)
--- a/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/.Depend
+++ b/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DEulerAngleTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DEulerAngleTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DEulerAngleTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DEulerAngleTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,30 +92,44 @@ matrix3DEulerAngleTransform.o: matrix3DEulerAngleTransform.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DEulerAngleTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DEulerAngleTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -96,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DEulerAngleTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DEulerAngleTransform.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DEulerAngleTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DEulerAngleTransform.h

diff --git a/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/Makefile b/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/Makefile
+++ b/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/matrix3DEulerAngleTransform b/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/matrix3DEulerAngleTransform
index ab66916..5cb57d1 100755 (executable)
Binary files a/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/matrix3DEulerAngleTransform and b/src/Tools/matrix3D/matrix3DEulerAngleTransform/src/X86MAC64/matrix3DEulerAngleTransform differ

diff --git a/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/.Depend b/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/.Depend
index 6e381b9..5eb0af5 100644 (file)
--- a/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/.Depend
+++ b/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DFromEulerAngle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DFromEulerAngle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DFromEulerAngle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DFromEulerAngle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,22 +91,39 @@ matrix3DFromEulerAngle.o: matrix3DFromEulerAngle.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DFromEulerAngle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DFromEulerAngle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h
@@ -87,34 +132,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DFromEulerAngle.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DFromEulerAngle.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DFromEulerAngle.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DFromEulerAngle.h

diff --git a/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/Makefile b/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/Makefile
+++ b/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/matrix3DFromEulerAngle b/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/matrix3DFromEulerAngle
index 5930a04..6d150ad 100755 (executable)
Binary files a/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/matrix3DFromEulerAngle and b/src/Tools/matrix3D/matrix3DFromEulerAngle/src/X86MAC64/matrix3DFromEulerAngle differ

diff --git a/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/.Depend b/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/.Depend
index 6bcd0fa..f0527c0 100644 (file)
--- a/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/.Depend
+++ b/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/matrix3DInverse.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DInverse.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/matrix3DInverse.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DInverse.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,64 +91,116 @@ matrix3DInverse.o: matrix3DInverse.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/matrix3DInverse.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DInverse.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h
+  /usr/include/sys/syslimits.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DInverse.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DInverse.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DInverse.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DInverse.h

diff --git a/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/Makefile b/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/Makefile
+++ b/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/matrix3DInverse b/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/matrix3DInverse
index 8e39040..33cc542 100755 (executable)
Binary files a/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/matrix3DInverse and b/src/Tools/matrix3D/matrix3DInverse/src/X86MAC64/matrix3DInverse differ

diff --git a/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/.Depend b/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/.Depend
index aa5dd27..261e9c4 100644 (file)
--- a/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/.Depend
+++ b/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DToEulerAngle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DToEulerAngle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DToEulerAngle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DToEulerAngle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,20 +91,38 @@ matrix3DToEulerAngle.o: matrix3DToEulerAngle.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/matrix3DToEulerAngle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/matrix3DToEulerAngle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -86,34 +132,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DToEulerAngle.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DToEulerAngle.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/matrix3DToEulerAngle.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/matrix3DToEulerAngle.h

diff --git a/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/Makefile b/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/Makefile
+++ b/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/matrix3DToEulerAngle b/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/matrix3DToEulerAngle
index 57e2bb8..6c81e7a 100755 (executable)
Binary files a/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/matrix3DToEulerAngle and b/src/Tools/matrix3D/matrix3DToEulerAngle/src/X86MAC64/matrix3DToEulerAngle differ

diff --git a/src/Tools/mrcImage/fft2d/src/X86MAC64/.Depend b/src/Tools/mrcImage/fft2d/src/X86MAC64/.Depend
index 7877893..ba0b8f6 100644 (file)
--- a/src/Tools/mrcImage/fft2d/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/fft2d/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/fft2d.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/fft2d.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ fft2d.o: fft2d.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/fft2d.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/fft2d.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -56,27 +90,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/fft2d.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/fft2d.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -85,32 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/fft2d.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/fft2d.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/fft2d.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/fft2d.h

diff --git a/src/Tools/mrcImage/fft2d/src/X86MAC64/Makefile b/src/Tools/mrcImage/fft2d/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/fft2d/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/fft2d/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/.Depend
index 3104f94..a506c9d 100644 (file)
--- a/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2dsn6.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2dsn6.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2dsn6.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2dsn6.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,29 +91,44 @@ mrc2dsn6.o: mrc2dsn6.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrc2dsn6.h /Applications/Eos.app/Eos/include/genUtil.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2dsn6.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -94,32 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2dsn6.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2dsn6.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2dsn6.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2dsn6.h

diff --git a/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrc2dsn6/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrc2map/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrc2map/src/X86MAC64/.Depend
index bc2b41f..b22b1f8 100644 (file)
--- a/src/Tools/mrcImage/mrc2map/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrc2map/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2map.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2map.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2map.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2map.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,29 +91,44 @@ mrc2map.o: mrc2map.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrc2map.h /Applications/Eos.app/Eos/include/genUtil.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2map.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -93,32 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2map.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2map.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2map.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2map.h

diff --git a/src/Tools/mrcImage/mrc2map/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrc2map/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrc2map/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrc2map/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrc2map/src/X86MAC64/mrc2map b/src/Tools/mrcImage/mrc2map/src/X86MAC64/mrc2map
index 5f41b5e..835acdf 100755 (executable)
Binary files a/src/Tools/mrcImage/mrc2map/src/X86MAC64/mrc2map and b/src/Tools/mrcImage/mrc2map/src/X86MAC64/mrc2map differ

diff --git a/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/.Depend
index 10def7e..716207c 100644 (file)
--- a/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc3DExtractZ.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc3DExtractZ.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc3DExtractZ.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc3DExtractZ.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrc3DExtractZ.o: mrc3DExtractZ.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc3DExtractZ.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc3DExtractZ.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrc3DExtractZ.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc3DExtractZ.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrc3DExtractZ.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc3DExtractZ.h

diff --git a/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/mrc3DExtractZ b/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/mrc3DExtractZ
index 6e65a07..45de2ac 100755 (executable)
Binary files a/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/mrc3DExtractZ and b/src/Tools/mrcImage/mrc3DExtractZ/src/X86MAC64/mrc3DExtractZ differ

diff --git a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/.Depend
index 06fd175..8fc96e5 100644 (file)
--- a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcFETnormalizeBySD.o: mrcFETnormalizeBySD.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcFETnormalizeBySD.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcFETnormalizeBySD.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFETnormalizeBySD.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFETnormalizeBySD.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFETnormalizeBySD.h

diff --git a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/mrcFETnormalizeBySD b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/mrcFETnormalizeBySD
index 57f26a2..5043a68 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/mrcFETnormalizeBySD and b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86MAC64/mrcFETnormalizeBySD differ

diff --git a/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/.Depend
index dd1ce4c..e98a7a1 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTBandPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTBandPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTBandPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTBandPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcFFTBandPassFilter.o: mrcFFTBandPassFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTBandPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTBandPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTBandPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTBandPassFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTBandPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTBandPassFilter.h

diff --git a/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/mrcFFTBandPassFilter b/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/mrcFFTBandPassFilter
index 5426a9e..09c3847 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/mrcFFTBandPassFilter and b/src/Tools/mrcImage/mrcFFTBandPassFilter/src/X86MAC64/mrcFFTBandPassFilter differ

diff --git a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/.Depend
index a02237a..4c999b8 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,18 +91,37 @@ mrcFFTCTFCompensation.o: mrcFFTCTFCompensation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/math.h ../inc/config.h \
   ../inc/../inc/mrcFFTCTFCompensation.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
@@ -82,41 +129,76 @@ mrcFFTCTFCompensation.o: mrcFFTCTFCompensation.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/String.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTCTFCompensation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTCTFCompensation.h

diff --git a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/mrcFFTCTFCompensation b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/mrcFFTCTFCompensation
index 6561501..dcffd9d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/mrcFFTCTFCompensation and b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86MAC64/mrcFFTCTFCompensation differ

diff --git a/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/.Depend
index cd65613..315e1a2 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTDigitize.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTDigitize.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTDigitize.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTDigitize.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcFFTDigitize.o: mrcFFTDigitize.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTDigitize.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTDigitize.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTDigitize.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTDigitize.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTDigitize.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTDigitize.h

diff --git a/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/mrcFFTDigitize b/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/mrcFFTDigitize
index 682bfd0..2466b55 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/mrcFFTDigitize and b/src/Tools/mrcImage/mrcFFTDigitize/src/X86MAC64/mrcFFTDigitize differ

diff --git a/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/.Depend
index d2fe6b0..7b5d400 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTExpression.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTExpression.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTExpression.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTExpression.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcFFTExpression.o: mrcFFTExpression.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTExpression.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTExpression.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcFFTExpression.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcFFTExpression.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTExpression.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTExpression.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTExpression.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTExpression.h

diff --git a/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/mrcFFTExpression b/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/mrcFFTExpression
index 40366f1..05bafa9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/mrcFFTExpression and b/src/Tools/mrcImage/mrcFFTExpression/src/X86MAC64/mrcFFTExpression differ

diff --git a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/.Depend
index 44f9177..e2b84b3 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcFFTFibreDiagram.o: mrcFFTFibreDiagram.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTFibreDiagram.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTFibreDiagram.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFibreDiagram.h

diff --git a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/mrcFFTFibreDiagram b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/mrcFFTFibreDiagram
index 16c529f..6206b2a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/mrcFFTFibreDiagram and b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86MAC64/mrcFFTFibreDiagram differ

diff --git a/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/.Depend
index d4460c3..7b08451 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,112 @@ mrcFFTFiltering.o: mrcFFTFiltering.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h
+  /Applications/Eos.app/Eos/include/Array.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTFiltering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFiltering.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTFiltering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTFiltering.h

diff --git a/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/mrcFFTFiltering b/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/mrcFFTFiltering
index d033e53..5756b32 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/mrcFFTFiltering and b/src/Tools/mrcImage/mrcFFTFiltering/src/X86MAC64/mrcFFTFiltering differ

diff --git a/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/.Depend
index 0b2c4e1..1342114 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,31 +91,46 @@ mrcFFTIQEstimation.o: mrcFFTIQEstimation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -95,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTIQEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTIQEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTIQEstimation.h

diff --git a/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/mrcFFTIQEstimation b/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/mrcFFTIQEstimation
index 2aadad6..878e9a6 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/mrcFFTIQEstimation and b/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86MAC64/mrcFFTIQEstimation differ

diff --git a/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/.Depend
index 884d40c..38d6eb3 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,113 @@ mrcFFTInfo.o: mrcFFTInfo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTInfo.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcFFTInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcFFTInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTInfo.h

diff --git a/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/mrcFFTInfo b/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/mrcFFTInfo
index e84bffe..4544844 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/mrcFFTInfo and b/src/Tools/mrcImage/mrcFFTInfo/src/X86MAC64/mrcFFTInfo differ

diff --git a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/.Depend
index 7511cf5..675157b 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTLayerLineCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTLayerLineCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTLayerLineCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTLayerLineCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcFFTLayerLineCheck.o: mrcFFTLayerLineCheck.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFFTLayerLineCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTLayerLineCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTLayerLineCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTLayerLineCheck.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTLayerLineCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTLayerLineCheck.h

diff --git a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/mrcFFTLayerLineCheck b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/mrcFFTLayerLineCheck
index c6b47af..4bbc408 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/mrcFFTLayerLineCheck and b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86MAC64/mrcFFTLayerLineCheck differ

diff --git a/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/.Depend
index 4c239c2..7a46513 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,31 +91,46 @@ mrcFFTMedianFilter.o: mrcFFTMedianFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -94,34 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTMedianFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTMedianFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTMedianFilter.h

diff --git a/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/mrcFFTMedianFilter b/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/mrcFFTMedianFilter
index 174ae9b..51e4db7 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/mrcFFTMedianFilter and b/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86MAC64/mrcFFTMedianFilter differ

diff --git a/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/.Depend
index 11a26c3..eb6166f 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,114 @@ mrcFFTProjection.o: mrcFFTProjection.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTProjection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTProjection.h

diff --git a/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/mrcFFTProjection b/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/mrcFFTProjection
index 823f2b0..1364f53 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/mrcFFTProjection and b/src/Tools/mrcImage/mrcFFTProjection/src/X86MAC64/mrcFFTProjection differ

diff --git a/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/.Depend
index 1f784c9..17a50f8 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTResampling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTResampling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTResampling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTResampling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcFFTResampling.o: mrcFFTResampling.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTResampling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTResampling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTResampling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTResampling.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTResampling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTResampling.h

diff --git a/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/mrcFFTResampling b/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/mrcFFTResampling
index 4f5bb30..69ddda0 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/mrcFFTResampling and b/src/Tools/mrcImage/mrcFFTResampling/src/X86MAC64/mrcFFTResampling differ

diff --git a/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/.Depend
index bf05e82..66ee9e1 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcFFTShellInfo.o: mrcFFTShellInfo.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTShellInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTShellInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTShellInfo.h

diff --git a/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/mrcFFTShellInfo b/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/mrcFFTShellInfo
index d17a7f4..e992cea 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/mrcFFTShellInfo and b/src/Tools/mrcImage/mrcFFTShellInfo/src/X86MAC64/mrcFFTShellInfo differ

diff --git a/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/.Depend
index 2d6e56e..c48dfda 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcFFTSizeChange.o: mrcFFTSizeChange.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTSizeChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTSizeChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSizeChange.h

diff --git a/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/mrcFFTSizeChange b/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/mrcFFTSizeChange
index 2297de1..7fd9bad 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/mrcFFTSizeChange and b/src/Tools/mrcImage/mrcFFTSizeChange/src/X86MAC64/mrcFFTSizeChange differ

diff --git a/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/.Depend
index c1864ff..5130b73 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,114 @@ mrcFFTSpectrum.o: mrcFFTSpectrum.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTSpectrum.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTSpectrum.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTSpectrum.h

diff --git a/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/mrcFFTSpectrum b/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/mrcFFTSpectrum
index 4f6c4aa..0189f99 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/mrcFFTSpectrum and b/src/Tools/mrcImage/mrcFFTSpectrum/src/X86MAC64/mrcFFTSpectrum differ

diff --git a/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/.Depend
index 81c2e68..5cf368e 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcFFTXFiltering.o: mrcFFTXFiltering.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcFFTInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTXFiltering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTXFiltering.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTXFiltering.h

diff --git a/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/mrcFFTXFiltering b/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/mrcFFTXFiltering
index add48e4..3edf450 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/mrcFFTXFiltering and b/src/Tools/mrcImage/mrcFFTXFiltering/src/X86MAC64/mrcFFTXFiltering differ

diff --git a/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/.Depend
index 087e29a..45becb7 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcFFTplainreduce.o: mrcFFTplainreduce.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTplainreduce.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFFTplainreduce.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFFTplainreduce.h

diff --git a/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/mrcFFTplainreduce b/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/mrcFFTplainreduce
index 6e79a81..05e6581 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/mrcFFTplainreduce and b/src/Tools/mrcImage/mrcFFTplainreduce/src/X86MAC64/mrcFFTplainreduce differ

diff --git a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/.Depend
index f97a741..3bcdae5 100644 (file)
--- a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFTMeridianEquatorRedece.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFTMeridianEquatorRedece.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFTMeridianEquatorRedece.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFTMeridianEquatorRedece.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcFTMeridianEquatorRedece.o: mrcFTMeridianEquatorRedece.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcFTMeridianEquatorRedece.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcFTMeridianEquatorRedece.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFTMeridianEquatorRedece.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFTMeridianEquatorRedece.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcFTMeridianEquatorRedece.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcFTMeridianEquatorRedece.h

diff --git a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/mrcFTMeridianEquatorRedece b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/mrcFTMeridianEquatorRedece
index baba46d..a2cc55e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/mrcFTMeridianEquatorRedece and b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86MAC64/mrcFTMeridianEquatorRedece differ

diff --git a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/.Depend
index 9cb4008..7ff416a 100644 (file)
--- a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1DProjectionfrom2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1DProjectionfrom2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1DProjectionfrom2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1DProjectionfrom2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImage1DProjectionfrom2D.o: mrcImage1DProjectionfrom2D.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1DProjectionfrom2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1DProjectionfrom2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1DProjectionfrom2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1DProjectionfrom2D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1DProjectionfrom2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1DProjectionfrom2D.h

diff --git a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/mrcImage1DProjectionfrom2D b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/mrcImage1DProjectionfrom2D
index 7f83b1f..86dd092 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/mrcImage1DProjectionfrom2D and b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86MAC64/mrcImage1DProjectionfrom2D differ

diff --git a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/.Depend
index 4148adb..67c41f1 100644 (file)
--- a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dAverageByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dAverageByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dAverageByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dAverageByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImage1dAverageByCorrelation.o: mrcImage1dAverageByCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dAverageByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dAverageByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dAverageByCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dAverageByCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dAverageByCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dAverageByCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/mrcImage1dAverageByCorrelation b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/mrcImage1dAverageByCorrelation
index 7cc6be4..5af4a8f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/mrcImage1dAverageByCorrelation and b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86MAC64/mrcImage1dAverageByCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/.Depend
index b6d5a23..c5fea45 100644 (file)
--- a/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dCutAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dCutAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dCutAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dCutAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImage1dCutAverage.o: mrcImage1dCutAverage.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dCutAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dCutAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dCutAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dCutAverage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dCutAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dCutAverage.h

diff --git a/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage1dCutAverage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/.Depend
index d139f40..7345263 100644 (file)
--- a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,20 +92,38 @@ mrcImage1dShiftAverageByAnnealing.o: mrcImage1dShiftAverageByAnnealing.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -87,42 +133,79 @@ mrcImage1dShiftAverageByAnnealing.o: mrcImage1dShiftAverageByAnnealing.c \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
   /Applications/Eos.app/Eos/include/mrcImagefuncmin.h \
   /Applications/Eos.app/Eos/include/nr2.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftAverageByAnnealing.h

diff --git a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/mrcImage1dShiftAverageByAnnealing b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/mrcImage1dShiftAverageByAnnealing
index aa02f0c..6862fcc 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/mrcImage1dShiftAverageByAnnealing and b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86MAC64/mrcImage1dShiftAverageByAnnealing differ

diff --git a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/.Depend
index 80acccc..89d824b 100644 (file)
--- a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImage1dShiftByCorrelation.o: mrcImage1dShiftByCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -92,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftByCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftByCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage1dShiftByCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage1dShiftByCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/mrcImage1dShiftByCorrelation b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/mrcImage1dShiftByCorrelation
index e9af4af..63acefa 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/mrcImage1dShiftByCorrelation and b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86MAC64/mrcImage1dShiftByCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/.Depend
index 5c31e3c..94fc420 100644 (file)
--- a/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DBackProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DBackProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DBackProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DBackProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImage2DBackProjection.o: mrcImage2DBackProjection.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DBackProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DBackProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DBackProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DBackProjection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DBackProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DBackProjection.h

diff --git a/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/mrcImage2DBackProjection b/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/mrcImage2DBackProjection
index 238fd01..c461ad0 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/mrcImage2DBackProjection and b/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86MAC64/mrcImage2DBackProjection differ

diff --git a/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/.Depend
index 061539a..830bf46 100644 (file)
--- a/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImage2DProjection.o: mrcImage2DProjection.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DProjection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage2DProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage2DProjection.h

diff --git a/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/mrcImage2DProjection b/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/mrcImage2DProjection
index 85b00c3..a66cf1c 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/mrcImage2DProjection and b/src/Tools/mrcImage/mrcImage2DProjection/src/X86MAC64/mrcImage2DProjection differ

diff --git a/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/.Depend
index 129f759..2d7a180 100644 (file)
--- a/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage2pdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2pdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage2pdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2pdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,118 @@ mrcImage2pdb.o: mrcImage2pdb.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage2pdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage2pdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/mrcRefUtil.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /Applications/Eos.app/Eos/include/mrcRefUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImage2pdb.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage2pdb.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImage2pdb.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage2pdb.h

diff --git a/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/mrcImage2pdb b/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/mrcImage2pdb
index 76ef416..60e016f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/mrcImage2pdb and b/src/Tools/mrcImage/mrcImage2pdb/src/X86MAC64/mrcImage2pdb differ

diff --git a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/.Depend
index f239917..fce84fc 100644 (file)
--- a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DHighResoEmphasis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DHighResoEmphasis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DHighResoEmphasis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DHighResoEmphasis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImage3DHighResoEmphasis.o: mrcImage3DHighResoEmphasis.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DHighResoEmphasis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DHighResoEmphasis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DHighResoEmphasis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DHighResoEmphasis.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DHighResoEmphasis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DHighResoEmphasis.h

diff --git a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/mrcImage3DHighResoEmphasis b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/mrcImage3DHighResoEmphasis
index c379a15..d5a174e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/mrcImage3DHighResoEmphasis and b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86MAC64/mrcImage3DHighResoEmphasis differ

diff --git a/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/.Depend
index f657260..3e3717b 100644 (file)
--- a/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImage3DPad.o: mrcImage3DPad.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DPad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DPad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad.h

diff --git a/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/mrcImage3DPad b/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/mrcImage3DPad
index bde2723..d66e7eb 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/mrcImage3DPad and b/src/Tools/mrcImage/mrcImage3DPad/src/X86MAC64/mrcImage3DPad differ

diff --git a/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/.Depend
index c766213..27bb02f 100644 (file)
--- a/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImage3DPad.o: mrcImage3DPad.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,22 +134,40 @@ mrcImage3DPad2.o: mrcImage3DPad2.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad2.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -111,34 +177,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DPad2.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad2.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DPad2.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DPad2.h

diff --git a/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/mrcImage3DPad2 b/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/mrcImage3DPad2
index 5ef357b..7a1f729 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/mrcImage3DPad2 and b/src/Tools/mrcImage/mrcImage3DPad2/src/X86MAC64/mrcImage3DPad2 differ

diff --git a/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/.Depend
index 78b84f5..6fa0c93 100644 (file)
--- a/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DSymmetryFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DSymmetryFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DSymmetryFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DSymmetryFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,61 +91,113 @@ mrcImage3DSymmetryFind.o: mrcImage3DSymmetryFind.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DSymmetryFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DSymmetryFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
+  /Applications/Eos.app/Eos/include/Array.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DSymmetryFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DSymmetryFind.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DSymmetryFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DSymmetryFind.h

diff --git a/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/mrcImage3DSymmetryFind b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/mrcImage3DSymmetryFind
new file mode 100755 (executable)
index 0000000..a37390c
Binary files /dev/null and b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/X86MAC64/mrcImage3DSymmetryFind differ

diff --git a/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/.Depend
index e73ee09..1a4fe7b 100644 (file)
--- a/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImage3DWindowing.o: mrcImage3DWindowing.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImage3DWindowing.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImage3DWindowing.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DWindowing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImage3DWindowing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImage3DWindowing.h

diff --git a/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/mrcImage3DWindowing b/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/mrcImage3DWindowing
index b159c34..b106fc2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/mrcImage3DWindowing and b/src/Tools/mrcImage/mrcImage3DWindowing/src/X86MAC64/mrcImage3DWindowing differ

diff --git a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/.Depend
index 2f5d55c..af52b0c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAbnormalValueRemove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAbnormalValueRemove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAbnormalValueRemove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAbnormalValueRemove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,24 +92,44 @@ mrcImageAbnormalValueRemove.o: mrcImageAbnormalValueRemove.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAbnormalValueRemove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAbnormalValueRemove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAbnormalValueRemove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAbnormalValueRemove.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAbnormalValueRemove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAbnormalValueRemove.h

diff --git a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/mrcImageAbnormalValueRemove b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/mrcImageAbnormalValueRemove
index bd6dcd0..4c4ccd9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/mrcImageAbnormalValueRemove and b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86MAC64/mrcImageAbnormalValueRemove differ

diff --git a/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/.Depend
index e4578f9..fb3dd98 100644 (file)
--- a/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageActinSingleParticleAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageActinSingleParticleAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +47,85 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageActinSingleParticleAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageActinSingleParticleAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageActinSingleParticleAnalysis.o:  \
- mrcImageActinSingleParticleAnalysis.c /usr/include/stdio.h \
+mrcImageActinSingleParticleAnalysis.o: \
+  mrcImageActinSingleParticleAnalysis.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageActinSingleParticleAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageActinSingleParticleAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageActinSingleParticleAnalysis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageActinSingleParticleAnalysis.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageActinSingleParticleAnalysis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageActinSingleParticleAnalysis.h

diff --git a/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/mrcImageActinSingleParticleAnalysis b/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/mrcImageActinSingleParticleAnalysis
index 1428620..a133bbf 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/mrcImageActinSingleParticleAnalysis and b/src/Tools/mrcImage/mrcImageActinSingleParticleAnalysis/src/X86MAC64/mrcImageActinSingleParticleAnalysis differ

diff --git a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/.Depend
index 51d8174..72e309a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAdaptiveBinalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdaptiveBinalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAdaptiveBinalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdaptiveBinalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,22 +92,40 @@ mrcImageAdaptiveBinalization.o: mrcImageAdaptiveBinalization.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/genUtil.h \
-  ../inc/config.h ../inc/../inc/mrcImageAdaptiveBinalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/genUtil.h ../inc/config.h \
+  ../inc/../inc/mrcImageAdaptiveBinalization.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAdaptiveBinalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdaptiveBinalization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAdaptiveBinalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdaptiveBinalization.h

diff --git a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/mrcImageAdaptiveBinalization b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/mrcImageAdaptiveBinalization
index eef3308..abba9b6 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/mrcImageAdaptiveBinalization and b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86MAC64/mrcImageAdaptiveBinalization differ

diff --git a/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/.Depend
index ebbc311..2eddc66 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,68 +91,120 @@ mrcImageAdd.o: mrcImageAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAdd.h

diff --git a/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/mrcImageAdd b/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/mrcImageAdd
index c674901..4fee6bd 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/mrcImageAdd and b/src/Tools/mrcImage/mrcImageAdd/src/X86MAC64/mrcImageAdd differ

diff --git a/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/.Depend
index ea80f76..1c3b499 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAddValue.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAddValue.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAddValue.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAddValue.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageAddValue.o: mrcImageAddValue.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAddValue.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAddValue.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageAddValue.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageAddValue.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAddValue.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAddValue.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAddValue.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAddValue.h

diff --git a/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/mrcImageAddValue b/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/mrcImageAddValue
index 69d4970..6c3f333 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/mrcImageAddValue and b/src/Tools/mrcImage/mrcImageAddValue/src/X86MAC64/mrcImageAddValue differ

diff --git a/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/.Depend
index a9d073a..8c41ad9 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageAreaCalc.o: mrcImageAreaCalc.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageCalcArea.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageCalcArea.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAreaCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAreaCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAreaCalc.h

diff --git a/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/mrcImageAreaCalc b/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/mrcImageAreaCalc
index c2ee8e5..e3d7339 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/mrcImageAreaCalc and b/src/Tools/mrcImage/mrcImageAreaCalc/src/X86MAC64/mrcImageAreaCalc differ

diff --git a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/.Depend
index 6a5813b..1325f92 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAssignedToTFofPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAssignedToTFofPDB.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAssignedToTFofPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAssignedToTFofPDB.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,61 +92,114 @@ mrcImageAssignedToTFofPDB.o: mrcImageAssignedToTFofPDB.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAssignedToTFofPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAssignedToTFofPDB.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/pdbFile.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAssignedToTFofPDB.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAssignedToTFofPDB.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAssignedToTFofPDB.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAssignedToTFofPDB.h

diff --git a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/mrcImageAssignedToTFofPDB b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/mrcImageAssignedToTFofPDB
index 40c0167..59d91e6 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/mrcImageAssignedToTFofPDB and b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86MAC64/mrcImageAssignedToTFofPDB differ

diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/.Depend
index 7daa04a..9c77c81 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +47,85 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageAutoCorrelationWithWindowing.o:  \
- mrcImageAutoCorrelationWithWindowing.c /usr/include/stdio.h \
+mrcImageAutoCorrelationWithWindowing.o: \
+  mrcImageAutoCorrelationWithWindowing.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoCorrelationWithWindowing.h

diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/mrcImageAutoCorrelationWithWindowing b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/mrcImageAutoCorrelationWithWindowing
index 02a63b1..10cb5d0 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/mrcImageAutoCorrelationWithWindowing and b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86MAC64/mrcImageAutoCorrelationWithWindowing differ

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/.Depend
index 73c2f41..05e7e1a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoFilamentExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoFilamentExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoFilamentExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoFilamentExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageAutoFilamentExtract.o: mrcImageAutoFilamentExtract.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoFilamentExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoFilamentExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoFilamentExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoFilamentExtract.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoFilamentExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoFilamentExtract.h

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/mrcImageAutoFilamentExtract b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/mrcImageAutoFilamentExtract
index b94f5b7..de07b2f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/mrcImageAutoFilamentExtract and b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86MAC64/mrcImageAutoFilamentExtract differ

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/.Depend
index d597683..665040b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoFilamentExtractResultAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +48,87 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoFilamentExtractResultAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageAutoFilamentExtractResultAnalysis.o:  \
- mrcImageAutoFilamentExtractResultAnalysis.c /usr/include/stdio.h \
+mrcImageAutoFilamentExtractResultAnalysis.o: \
+  mrcImageAutoFilamentExtractResultAnalysis.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoFilamentExtractResultAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +139,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoFilamentExtractResultAnalysis.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoFilamentExtractResultAnalysis.h

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/mrcImageAutoFilamentExtractResultAnalysis b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/mrcImageAutoFilamentExtractResultAnalysis
index 09c05d1..1e0b176 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/mrcImageAutoFilamentExtractResultAnalysis and b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86MAC64/mrcImageAutoFilamentExtractResultAnalysis differ

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/.Depend
index 7b10c10..fee7eb9 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,29 +92,45 @@ mrcImageAutoRotationCorrelation.o: mrcImageAutoRotationCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageCorrelation.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/PVM.h \
   /Applications/Eos.app/Eos/include/lmrcImageSSDA.h \
   /Applications/Eos.app/Eos/include/lmrcImageROI2D.h \
@@ -96,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/mrcImageAutoRotationCorrelation b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/mrcImageAutoRotationCorrelation
index 26b1b36..7b2203c 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/mrcImageAutoRotationCorrelation and b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86MAC64/mrcImageAutoRotationCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/.Depend
index 3350dc5..c9e1c9b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,29 +92,45 @@ mrcImageAutoRotationCorrelation3D.o: mrcImageAutoRotationCorrelation3D.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageCorrelation.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/PVM.h \
   /Applications/Eos.app/Eos/include/lmrcImageSSDA.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -94,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation3D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAutoRotationCorrelation3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAutoRotationCorrelation3D.h

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/mrcImageAutoRotationCorrelation3D b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/mrcImageAutoRotationCorrelation3D
index b6c347b..cca0497 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/mrcImageAutoRotationCorrelation3D and b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86MAC64/mrcImageAutoRotationCorrelation3D differ

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/.Depend
index da5228b..01bc733 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoRotationCorrelationResultPrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,60 +48,92 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoRotationCorrelationResultPrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageAutoRotationCorrelationResultPrint.o:  \
- mrcImageAutoRotationCorrelationResultPrint.c /usr/include/stdio.h \
+mrcImageAutoRotationCorrelationResultPrint.o: \
+  mrcImageAutoRotationCorrelationResultPrint.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoRotationCorrelationResultPrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageCorrelation.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/PVM.h \
   /Applications/Eos.app/Eos/include/lmrcImageSSDA.h \
   /Applications/Eos.app/Eos/include/lmrcImageROI2D.h \
@@ -96,34 +143,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoRotationCorrelationResultPrint.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageAutoRotationCorrelationResultPrint.h

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/.Depend
old mode 100755 (executable)
new mode 100644 (file)
index 4884633..38f88cc
--- a/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,67 +93,117 @@ mrcImageAverage.o: mrcImageAverage.c \
   /usr/include/AvailabilityInternal.h /usr/include/stdio.h \
   /usr/include/_types.h /usr/include/sys/_types.h \
   /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
-  /usr/include/stdlib.h /usr/include/sys/wait.h /usr/include/sys/signal.h \
+  /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h \
+  /usr/include/sys/_types/_null.h /usr/include/sys/_types/_off_t.h \
+  /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \
+  /usr/include/secure/_common.h /usr/include/stdlib.h \
+  /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h \
+  /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h \
   /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/signal.h /usr/include/machine/_mcontext.h \
+  /usr/include/i386/_mcontext.h /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  ../inc/config.h ../inc/../inc/mrcImageAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h ../inc/config.h \
+  ../inc/../inc/mrcImageAverage.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageAverage.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageAverage.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAverage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageAverage.h

diff --git a/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/mrcImageAverage b/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/mrcImageAverage
index ef68cf4..fd2c6ee 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/mrcImageAverage and b/src/Tools/mrcImage/mrcImageAverage/src/X86MAC64/mrcImageAverage differ

diff --git a/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/.Depend
old mode 100755 (executable)
new mode 100644 (file)
index e205c56..c14b82d
--- a/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBandPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBandPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBandPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBandPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,20 +91,38 @@ mrcImageBandPassFilter.o: mrcImageBandPassFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBandPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBandPassFilter.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -88,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBandPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBandPassFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBandPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBandPassFilter.h

diff --git a/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/mrcImageBandPassFilter b/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/mrcImageBandPassFilter
index a424941..463a926 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/mrcImageBandPassFilter and b/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86MAC64/mrcImageBandPassFilter differ

diff --git a/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/.Depend
index 3828154..9c75fac 100644 (file)
--- a/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBilateralFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBilateralFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBilateralFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBilateralFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,62 +91,114 @@ mrcImageBilateralFilter.o: mrcImageBilateralFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBilateralFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBilateralFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageBilateralFilter.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageBilateralFilter.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBilateralFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBilateralFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBilateralFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBilateralFilter.h

diff --git a/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/mrcImageBilateralFilter b/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/mrcImageBilateralFilter
index b952a19..b0beebc 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/mrcImageBilateralFilter and b/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86MAC64/mrcImageBilateralFilter differ

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/.Depend
index 1091b6a..2bd5046 100644 (file)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBinalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBinalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBinalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBinalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,62 +91,114 @@ mrcImageBinalization.o: mrcImageBinalization.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBinalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBinalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageBinarization.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageBinarization.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBinalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBinalization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBinalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBinalization.h

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/mrcImageBinalization b/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/mrcImageBinalization
index 9467881..0c844ad 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/mrcImageBinalization and b/src/Tools/mrcImage/mrcImageBinalization/src/X86MAC64/mrcImageBinalization differ

diff --git a/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/.Depend
index 0a7fd69..d40340f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageBlockMerge.o: mrcImageBlockMerge.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBlockMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBlockMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBlockMerge.h

diff --git a/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/mrcImageBlockMerge b/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/mrcImageBlockMerge
index e358fc9..0fca7c2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/mrcImageBlockMerge and b/src/Tools/mrcImage/mrcImageBlockMerge/src/X86MAC64/mrcImageBlockMerge differ

diff --git a/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/.Depend
index 4afdd1f..4a40706 100644 (file)
--- a/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBoundaryInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBoundaryInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBoundaryInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBoundaryInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageBoundaryInfo.o: mrcImageBoundaryInfo.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageBoundaryInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageBoundaryInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBoundaryInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBoundaryInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageBoundaryInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageBoundaryInfo.h

diff --git a/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/mrcImageBoundaryInfo b/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/mrcImageBoundaryInfo
index 1428620..a133bbf 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/mrcImageBoundaryInfo and b/src/Tools/mrcImage/mrcImageBoundaryInfo/src/X86MAC64/mrcImageBoundaryInfo differ

diff --git a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/.Depend
index 32c74bf..d083852 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCCDNoiseRemove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCCDNoiseRemove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCCDNoiseRemove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCCDNoiseRemove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,32 +91,46 @@ mrcImageCCDNoiseRemove.o: mrcImageCCDNoiseRemove.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCCDNoiseRemove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCCDNoiseRemove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h
@@ -97,34 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCCDNoiseRemove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCCDNoiseRemove.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCCDNoiseRemove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCCDNoiseRemove.h

diff --git a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/mrcImageCCDNoiseRemove b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/mrcImageCCDNoiseRemove
index f013efe..865410d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/mrcImageCCDNoiseRemove and b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86MAC64/mrcImageCCDNoiseRemove differ

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/.Depend
index eb3b6e3..9dfc346 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,73 +91,119 @@ mrcImageCTFCompensation.o: mrcImageCTFCompensation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensation.h \
-  /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensation.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lmrcImageCTFCompensation.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageCTFCompensation.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensation.h

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/mrcImageCTFCompensation b/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/mrcImageCTFCompensation
index f685a08..73066e5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/mrcImageCTFCompensation and b/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86MAC64/mrcImageCTFCompensation differ

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/.Depend
index 660cdfb..88a392f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensationForTiltImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensationForTiltImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,69 +47,95 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensationForTiltImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensationForTiltImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageCTFCompensationForTiltImage.o:  \
- mrcImageCTFCompensationForTiltImage.c /usr/include/stdio.h \
+mrcImageCTFCompensationForTiltImage.o: \
+  mrcImageCTFCompensationForTiltImage.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensationForTiltImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensationForTiltImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/lmrcImageROI2D.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageMontage.h \
   /Applications/Eos.app/Eos/include/lmrcImagePad.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -104,34 +144,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensationForTiltImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensationForTiltImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFCompensationForTiltImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFCompensationForTiltImage.h

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/mrcImageCTFCompensationForTiltImage b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/mrcImageCTFCompensationForTiltImage
index aabb20c..91492e9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/mrcImageCTFCompensationForTiltImage and b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/mrcImageCTFCompensationForTiltImage differ

diff --git a/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/.Depend
index d40c923..772fe07 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFDetermination.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFDetermination.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFDetermination.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFDetermination.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,39 +92,51 @@ mrcImageCTFDetermination.o: mrcImageCTFDetermination.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFDetermination.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFDetermination.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageCTFDetermination.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lllDataCTFCompensate.h \
   /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/lll2ltlg.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
@@ -107,7 +147,6 @@ mrcImageCTFDetermination.o: mrcImageCTFDetermination.c \
   /Applications/Eos.app/Eos/include/lmrcImageCrystalCreate.h \
   /Applications/Eos.app/Eos/include/lllExtractdYEstimate.h \
   /Applications/Eos.app/Eos/include/lmrcImagePad.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllExtractCtfinfFileCreate.h \
   /Applications/Eos.app/Eos/include/ctfZeroPoint.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -115,34 +154,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFDetermination.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFDetermination.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFDetermination.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFDetermination.h

diff --git a/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/mrcImageCTFDetermination b/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/mrcImageCTFDetermination
index 187f3c1..cfeb480 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/mrcImageCTFDetermination and b/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86MAC64/mrcImageCTFDetermination differ

diff --git a/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/.Depend
index 5eab7b5..0ce7a10 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFObservation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFObservation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFObservation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFObservation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,69 +91,118 @@ mrcImageCTFObservation.o: mrcImageCTFObservation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFObservation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFObservation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
+  /Applications/Eos.app/Eos/include/Array.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFObservation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFObservation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFObservation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFObservation.h

diff --git a/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/mrcImageCTFObservation b/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/mrcImageCTFObservation
index af36cdf..8f26a67 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/mrcImageCTFObservation and b/src/Tools/mrcImage/mrcImageCTFObservation/src/X86MAC64/mrcImageCTFObservation differ

diff --git a/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/.Depend
index 7d38461..279de8a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCTFSN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFSN.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCTFSN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFSN.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageCTFSN.o: mrcImageCTFSN.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCTFSN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFSN.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFSN.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFSN.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCTFSN.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCTFSN.h

diff --git a/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/mrcImageCTFSN b/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/mrcImageCTFSN
index 93caaf2..6e7568d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/mrcImageCTFSN and b/src/Tools/mrcImage/mrcImageCTFSN/src/X86MAC64/mrcImageCTFSN differ

diff --git a/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/.Depend
index 0359ea4..ffaacfe 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCVE.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCVE.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCVE.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCVE.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageCVE.o: mrcImageCVE.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCVE.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCVE.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,32 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageCVE.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCVE.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageCVE.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCVE.h

diff --git a/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/mrcImageCVE b/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/mrcImageCVE
index afc5079..1b8caf2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/mrcImageCVE and b/src/Tools/mrcImage/mrcImageCVE/src/X86MAC64/mrcImageCVE differ

diff --git a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/.Depend
index 06534a5..2aa93f6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterDensityChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterDensityChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterDensityChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterDensityChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageCenterDensityChange.o: mrcImageCenterDensityChange.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterDensityChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterDensityChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterDensityChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterDensityChange.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterDensityChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterDensityChange.h

diff --git a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/mrcImageCenterDensityChange b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/mrcImageCenterDensityChange
index 02527a9..c8d1b19 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/mrcImageCenterDensityChange and b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86MAC64/mrcImageCenterDensityChange differ

diff --git a/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/.Depend
index 4633130..e5cd764 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageCenterGet.o: mrcImageCenterGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,22 +135,40 @@ mrcImageCenterGet2.o: mrcImageCenterGet2.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -113,34 +179,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterGet.h

diff --git a/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/mrcImageCenterGet b/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/mrcImageCenterGet
index dc04753..4fe8215 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/mrcImageCenterGet and b/src/Tools/mrcImage/mrcImageCenterGet/src/X86MAC64/mrcImageCenterGet differ

diff --git a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/.Depend
index 41bef4a..240bd33 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterOfMassCalculate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterOfMassCalculate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterOfMassCalculate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterOfMassCalculate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcImageCenterOfMassCalculate.o: mrcImageCenterOfMassCalculate.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterOfMassCalculate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterOfMassCalculate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageCentre.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageCentre.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterOfMassCalculate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterOfMassCalculate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCenterOfMassCalculate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCenterOfMassCalculate.h

diff --git a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/mrcImageCenterOfMassCalculate b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/mrcImageCenterOfMassCalculate
index c202013..c7c1f5c 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/mrcImageCenterOfMassCalculate and b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86MAC64/mrcImageCenterOfMassCalculate differ

diff --git a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/.Depend
index 604ca50..25f8d8a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCircumferentialProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCircumferentialProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCircumferentialProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCircumferentialProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageCircumferentialProjection.o: mrcImageCircumferentialProjection.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCircumferentialProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCircumferentialProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCircumferentialProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCircumferentialProjection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCircumferentialProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCircumferentialProjection.h

diff --git a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/mrcImageCircumferentialProjection b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/mrcImageCircumferentialProjection
index 8e7a439..b4eb793 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/mrcImageCircumferentialProjection and b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86MAC64/mrcImageCircumferentialProjection differ

diff --git a/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/.Depend
index 9988ab6..856fa83 100644 (file)
--- a/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageClosing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageClosing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageClosing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageClosing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageClosing.o: mrcImageClosing.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageClosing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageClosing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageClosing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageClosing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageClosing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageClosing.h

diff --git a/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/mrcImageClosing b/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/mrcImageClosing
index 1acc137..59ef741 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/mrcImageClosing and b/src/Tools/mrcImage/mrcImageClosing/src/X86MAC64/mrcImageClosing differ

diff --git a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/.Depend
index 1800e8e..c8af65b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageClusterAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageClusterAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageClusterAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageClusterAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageClusterAnalysis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageClusterAnalysis.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageClusterAnalysis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageClusterAnalysis.h

diff --git a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/.Depend
index da87a09..7b01443 100644 (file)
--- a/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageColoring.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageColoring.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageColoring.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageColoring.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageColoring.o: mrcImageColoring.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageColoring.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageColoring.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -81,42 +130,76 @@ mrcImageColoring.o: mrcImageColoring.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/gifFile.h \
-  /Applications/Eos.app/Eos/include/gif_lib.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
+  /Applications/Eos.app/Eos/include/gif_lib.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageColoring.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageColoring.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageColoring.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageColoring.h

diff --git a/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/mrcImageColoring b/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/mrcImageColoring
index 825ee37..2c0d4e9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/mrcImageColoring and b/src/Tools/mrcImage/mrcImageColoring/src/X86MAC64/mrcImageColoring differ

diff --git a/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/.Depend
index ccf0ee4..068a2d5 100644 (file)
--- a/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageConnection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageConnection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageConnection.o: mrcImageConnection.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageConnection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnection.h \
   /Applications/Eos.app/Eos/include/lmrcImageConnection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
@@ -86,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageConnection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageConnection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnection.h

diff --git a/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/mrcImageConnection b/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/mrcImageConnection
index 98e3d02..e2e4120 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/mrcImageConnection and b/src/Tools/mrcImage/mrcImageConnection/src/X86MAC64/mrcImageConnection differ

diff --git a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/.Depend
index c965852..2ea8d63 100644 (file)
--- a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageConnectivityNumberCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnectivityNumberCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageConnectivityNumberCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnectivityNumberCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,63 +92,114 @@ mrcImageConnectivityNumberCalc.o: mrcImageConnectivityNumberCalc.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageConnectivityNumberCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnectivityNumberCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/mrcImageConnectivityNumberCalc.h \
-  /Applications/Eos.app/Eos/include/lmrcImageConnectivityNumberCalc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageConnectivityNumberCalc.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageConnectivityNumberCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnectivityNumberCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageConnectivityNumberCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageConnectivityNumberCalc.h

diff --git a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/mrcImageConnectivityNumberCalc b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/mrcImageConnectivityNumberCalc
index 800ee31..b3878df 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/mrcImageConnectivityNumberCalc and b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86MAC64/mrcImageConnectivityNumberCalc differ

diff --git a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/.Depend
index f209f0d..a85537b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageContourSurfaceCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageContourSurfaceCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageContourSurfaceCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageContourSurfaceCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcImageContourSurfaceCreate.o: mrcImageContourSurfaceCreate.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageContourSurfaceCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageContourSurfaceCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageContourSurface.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageContourSurface.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageContourSurfaceCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageContourSurfaceCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageContourSurfaceCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageContourSurfaceCreate.h

diff --git a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/mrcImageContourSurfaceCreate b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/mrcImageContourSurfaceCreate
index d87bd70..2924d67 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/mrcImageContourSurfaceCreate and b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86MAC64/mrcImageContourSurfaceCreate differ

diff --git a/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/.Depend
index 56ce5e6..725eff0 100644 (file)
--- a/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageConvolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConvolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageConvolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConvolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,114 @@ mrcImageConvolution.o: mrcImageConvolution.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageConvolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageConvolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/larray2mrc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/larray2mrc.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageConvolution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageConvolution.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageConvolution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageConvolution.h

diff --git a/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/mrcImageConvolution b/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/mrcImageConvolution
index 3967575..9e90754 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/mrcImageConvolution and b/src/Tools/mrcImage/mrcImageConvolution/src/X86MAC64/mrcImageConvolution differ

diff --git a/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/.Depend
index eb3ba47..3ff9e66 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoordinateChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoordinateChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoordinateChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoordinateChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageCoordinateChange.o: mrcImageCoordinateChange.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoordinateChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoordinateChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoordinateChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoordinateChange.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoordinateChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoordinateChange.h

diff --git a/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/mrcImageCoordinateChange b/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/mrcImageCoordinateChange
index ab41a70..02b337c 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/mrcImageCoordinateChange and b/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86MAC64/mrcImageCoordinateChange differ

diff --git a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/.Depend
index 061ebfa..5fce47f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoreImageCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoreImageCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoreImageCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoreImageCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,32 +91,45 @@ mrcImageCoreImageCalc.o: mrcImageCoreImageCalc.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoreImageCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoreImageCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -99,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoreImageCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoreImageCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCoreImageCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCoreImageCalc.h

diff --git a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/mrcImageCoreImageCalc b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/mrcImageCoreImageCalc
index 768d857..7466732 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/mrcImageCoreImageCalc and b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86MAC64/mrcImageCoreImageCalc differ

diff --git a/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/.Depend
old mode 100755 (executable)
new mode 100644 (file)
index 2628026..d0801ee
--- a/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageCorrelation.o: mrcImageCorrelation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelation.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -81,44 +130,78 @@ mrcImageCorrelation.o: mrcImageCorrelation.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageCorrelation.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/PVM.h \
   /Applications/Eos.app/Eos/include/lmrcImageSSDA.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/mrcImageCorrelation b/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/mrcImageCorrelation
index 84127e4..815aadb 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/mrcImageCorrelation and b/src/Tools/mrcImage/mrcImageCorrelation/src/X86MAC64/mrcImageCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/.Depend
index 370a439..d2c67c7 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationInFourierSpace.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationInFourierSpace.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationInFourierSpace.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationInFourierSpace.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageCorrelationInFourierSpace.o: mrcImageCorrelationInFourierSpace.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationInFourierSpace.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationInFourierSpace.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationInFourierSpace.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationInFourierSpace.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationInFourierSpace.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationInFourierSpace.h

diff --git a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/mrcImageCorrelationInFourierSpace b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/mrcImageCorrelationInFourierSpace
index b227118..4b2ab5b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/mrcImageCorrelationInFourierSpace and b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86MAC64/mrcImageCorrelationInFourierSpace differ

diff --git a/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/.Depend
index 13823ed..e8dc253 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,24 +92,41 @@ mrcImageCorrelationServer.o: mrcImageCorrelationServer.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lmrcImageCorrelation.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -93,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationServer.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCorrelationServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCorrelationServer.h

diff --git a/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCorrelationServer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/.Depend
index 112e4df..4393dec 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCrystalCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCrystalCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCrystalCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCrystalCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,61 +91,114 @@ mrcImageCrystalCreate.o: mrcImageCrystalCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCrystalCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCrystalCreate.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageCrystalCreate.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageCrystalCreate.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCrystalCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCrystalCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCrystalCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCrystalCreate.h

diff --git a/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/mrcImageCrystalCreate b/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/mrcImageCrystalCreate
index 80c4aa1..4a2fe33 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/mrcImageCrystalCreate and b/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86MAC64/mrcImageCrystalCreate differ

diff --git a/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/.Depend
index 6ba5136..395a8ce 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCutAndSetInArray.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCutAndSetInArray.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCutAndSetInArray.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCutAndSetInArray.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageCutAndSetInArray.o: mrcImageCutAndSetInArray.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCutAndSetInArray.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCutAndSetInArray.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCutAndSetInArray.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCutAndSetInArray.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCutAndSetInArray.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCutAndSetInArray.h

diff --git a/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/.Depend
index e7be487..38970a7 100644 (file)
--- a/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCylinderSection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCylinderSection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCylinderSection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCylinderSection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageCylinderSection.o: mrcImageCylinderSection.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCylinderSection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCylinderSection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCylinderSection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCylinderSection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCylinderSection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCylinderSection.h

diff --git a/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/mrcImageCylinderSection b/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/mrcImageCylinderSection
index bd4d320..2c955a5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/mrcImageCylinderSection and b/src/Tools/mrcImage/mrcImageCylinderSection/src/X86MAC64/mrcImageCylinderSection differ

diff --git a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/.Depend
index 5a270fc..3f6cb6c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDeadPixelCorrection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDeadPixelCorrection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDeadPixelCorrection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDeadPixelCorrection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,41 @@ mrcImageDeadPixelCorrection.o: mrcImageDeadPixelCorrection.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/nr2.h \
-  ../inc/config.h ../inc/../inc/mrcImageDeadPixelCorrection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/nr2.h ../inc/config.h \
+  ../inc/../inc/mrcImageDeadPixelCorrection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDeadPixelCorrection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDeadPixelCorrection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDeadPixelCorrection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDeadPixelCorrection.h

diff --git a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/mrcImageDeadPixelCorrection b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/mrcImageDeadPixelCorrection
index 0193d22..5c76954 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/mrcImageDeadPixelCorrection and b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86MAC64/mrcImageDeadPixelCorrection differ

diff --git a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/.Depend
index 114ed19..83fb6f9 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityChangeEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityChangeEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityChangeEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityChangeEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,71 +92,120 @@ mrcImageDensityChangeEstimation.o: mrcImageDensityChangeEstimation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityChangeEstimation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityChangeEstimation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageDensity.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageModeChange.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityChangeEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityChangeEstimation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityChangeEstimation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityChangeEstimation.h

diff --git a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/mrcImageDensityChangeEstimation b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/mrcImageDensityChangeEstimation
index 98f9c90..d2726b2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/mrcImageDensityChangeEstimation and b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86MAC64/mrcImageDensityChangeEstimation differ

diff --git a/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/.Depend
index 4ace0b3..b71774d 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,73 +91,120 @@ mrcImageDensityInfo.o: mrcImageDensityInfo.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageModeChange.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/lmrcImageDensity.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/lmrcImageModeChange.h \
-  /Applications/Eos.app/Eos/include/Vector.h
+  /Applications/Eos.app/Eos/include/lmrcImageDensity.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityInfo.h

diff --git a/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/mrcImageDensityInfo b/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/mrcImageDensityInfo
index 1481900..4fb12a1 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/mrcImageDensityInfo and b/src/Tools/mrcImage/mrcImageDensityInfo/src/X86MAC64/mrcImageDensityInfo differ

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/.Depend
index f701b43..23c0a7b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageDensityNormalization.o: mrcImageDensityNormalization.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalization.h

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/mrcImageDensityNormalization b/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/mrcImageDensityNormalization
index ed44b8e..31ada27 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/mrcImageDensityNormalization and b/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86MAC64/mrcImageDensityNormalization differ

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/.Depend
index baafb86..12ad8c2 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalizationByImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalizationByImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,93 +47,159 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalizationByImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalizationByImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageDensityNormalizationByImage.o:  \
- mrcImageDensityNormalizationByImage.c /usr/include/stdio.h \
+mrcImageDensityNormalizationByImage.o: \
+  mrcImageDensityNormalizationByImage.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalizationByImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalizationByImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageDensityNormalizationByImage.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageDensityNormalizationByImage.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalizationByImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalizationByImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDensityNormalizationByImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDensityNormalizationByImage.h

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/mrcImageDensityNormalizationByImage b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/mrcImageDensityNormalizationByImage
index 57a2971..b804d9b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/mrcImageDensityNormalizationByImage and b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86MAC64/mrcImageDensityNormalizationByImage differ

diff --git a/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/.Depend
index 9f9f950..112bee4 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageDilation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDilation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageDilation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDilation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageDilation.o: mrcImageDilation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageDilation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDilation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDilation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDilation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDilation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDilation.h

diff --git a/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/mrcImageDilation b/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/mrcImageDilation
index b898242..d33d596 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/mrcImageDilation and b/src/Tools/mrcImage/mrcImageDilation/src/X86MAC64/mrcImageDilation differ

diff --git a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/.Depend
index 5b05b0e..6f0690e 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,94 +47,160 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageDisplayDensityAsTempFactor.o:  \
- mrcImageDisplayDensityAsTempFactor.c /usr/include/stdio.h \
+mrcImageDisplayDensityAsTempFactor.o: \
+  mrcImageDisplayDensityAsTempFactor.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/pdbInfoGet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDisplayDensityAsTempFactor.h

diff --git a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/mrcImageDisplayDensityAsTempFactor b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/mrcImageDisplayDensityAsTempFactor
index 25a8c9b..b74fcea 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/mrcImageDisplayDensityAsTempFactor and b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86MAC64/mrcImageDisplayDensityAsTempFactor differ

diff --git a/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/.Depend
index f973667..145ff15 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDistanceConversion.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDistanceConversion.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDistanceConversion.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDistanceConversion.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,63 +92,114 @@ mrcImageDistanceConversion.o: mrcImageDistanceConversion.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDistanceConversion.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDistanceConversion.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/mrcImageDistanceConversion.h \
-  /Applications/Eos.app/Eos/include/lmrcImageDistanceConversion.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageDistanceConversion.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDistanceConversion.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDistanceConversion.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDistanceConversion.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDistanceConversion.h

diff --git a/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/mrcImageDistanceConversion b/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/mrcImageDistanceConversion
index 33d66e9..7d0480c 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/mrcImageDistanceConversion and b/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86MAC64/mrcImageDistanceConversion differ

diff --git a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/.Depend
index b39f975..a760862 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideInfoForTomography.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideInfoForTomography.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideInfoForTomography.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideInfoForTomography.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,32 +92,46 @@ mrcImageDivideInfoForTomography.o: mrcImageDivideInfoForTomography.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideInfoForTomography.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideInfoForTomography.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -98,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideInfoForTomography.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideInfoForTomography.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideInfoForTomography.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideInfoForTomography.h

diff --git a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/mrcImageDivideInfoForTomography b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/mrcImageDivideInfoForTomography
index ba18c8c..52e9b74 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/mrcImageDivideInfoForTomography and b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86MAC64/mrcImageDivideInfoForTomography differ

diff --git a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/.Depend
index 654102d..f3d5baf 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideIntoTwoImages.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideIntoTwoImages.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideIntoTwoImages.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideIntoTwoImages.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageDivideIntoTwoImages.o: mrcImageDivideIntoTwoImages.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideIntoTwoImages.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideIntoTwoImages.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideIntoTwoImages.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideIntoTwoImages.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageDivideIntoTwoImages.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageDivideIntoTwoImages.h

diff --git a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/mrcImageDivideIntoTwoImages b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/mrcImageDivideIntoTwoImages
index 6f5dd16..03d25b6 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/mrcImageDivideIntoTwoImages and b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86MAC64/mrcImageDivideIntoTwoImages differ

diff --git a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/.Depend
index 935f5f3..819589b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEdgeImageGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEdgeImageGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEdgeImageGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEdgeImageGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,31 +91,45 @@ mrcImageEdgeImageGet.o: mrcImageEdgeImageGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEdgeImageGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEdgeImageGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -97,34 +139,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageEdgeImageGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageEdgeImageGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageEdgeImageGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageEdgeImageGet.h

diff --git a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/mrcImageEdgeImageGet b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/mrcImageEdgeImageGet
index 9bae648..556c310 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/mrcImageEdgeImageGet and b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86MAC64/mrcImageEdgeImageGet differ

diff --git a/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/.Depend
index 31178f9..dfe670e 100644 (file)
--- a/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEnhancementWithFuzzySets.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEnhancementWithFuzzySets.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEnhancementWithFuzzySets.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEnhancementWithFuzzySets.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageEnhancementWithFuzzySets.o: mrcImageEnhancementWithFuzzySets.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEnhancementWithFuzzySets.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEnhancementWithFuzzySets.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageEnhancementWithFuzzySets.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageEnhancementWithFuzzySets.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageEnhancementWithFuzzySets.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageEnhancementWithFuzzySets.h

diff --git a/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/.Depend
index 0a42aba..7ef86b2 100644 (file)
--- a/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageErosion.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageErosion.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageErosion.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageErosion.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageErosion.o: mrcImageErosion.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageErosion.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageErosion.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageErosion.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageErosion.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageErosion.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageErosion.h

diff --git a/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/mrcImageErosion b/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/mrcImageErosion
index 50d9c54..9c73ab7 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/mrcImageErosion and b/src/Tools/mrcImage/mrcImageErosion/src/X86MAC64/mrcImageErosion differ

diff --git a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/.Depend
index bf6cf06..accc91b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEstimateTiltImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEstimateTiltImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEstimateTiltImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEstimateTiltImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,113 @@ mrcImageEstimateTiltImage.o: mrcImageEstimateTiltImage.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageEstimateTiltImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageEstimateTiltImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
+  /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageEstimateTiltImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageEstimateTiltImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageEstimateTiltImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageEstimateTiltImage.h

diff --git a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/mrcImageEstimateTiltImage b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/mrcImageEstimateTiltImage
index 2994254..075a5bc 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/mrcImageEstimateTiltImage and b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86MAC64/mrcImageEstimateTiltImage differ

diff --git a/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/.Depend
index 2fee5ab..48c3457 100644 (file)
--- a/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageExpression.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageExpression.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageExpression.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageExpression.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageExpression.o: mrcImageExpression.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageExpression.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageExpression.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageExpression.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageExpression.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageExpression.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageExpression.h

diff --git a/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/mrcImageExpression b/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/mrcImageExpression
index 1cbf798..ec8e813 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/mrcImageExpression and b/src/Tools/mrcImage/mrcImageExpression/src/X86MAC64/mrcImageExpression differ

diff --git a/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/.Depend
index 2cb3040..7b818b9 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFT.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFT.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageFFT.o: mrcImageFFT.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFT.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,32 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageFFT.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFT.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageFFT.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFT.h

diff --git a/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/mrcImageFFT b/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/mrcImageFFT
index d8dde68..87de9f4 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/mrcImageFFT and b/src/Tools/mrcImage/mrcImageFFT/src/X86MAC64/mrcImageFFT differ

diff --git a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/.Depend
index 5623dff..64797fb 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFFTLayerLineExtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFTLayerLineExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFFTLayerLineExtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFTLayerLineExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,24 +92,40 @@ mrcImageFFTLayerLineExtraction.o: mrcImageFFTLayerLineExtraction.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFFTLayerLineExtraction.h \
-  /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFTLayerLineExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -92,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFFTLayerLineExtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFTLayerLineExtraction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFFTLayerLineExtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFFTLayerLineExtraction.h

diff --git a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/mrcImageFFTLayerLineExtraction b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/mrcImageFFTLayerLineExtraction
index e5f6bb7..130c723 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/mrcImageFFTLayerLineExtraction and b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86MAC64/mrcImageFFTLayerLineExtraction differ

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/.Depend
index b538d85..d006421 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,69 +91,119 @@ mrcImageFOMCalc.o: mrcImageFOMCalc.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageFOMCalc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageFOMCalc.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFOMCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFOMCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/mrcImageFOMCalc b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/mrcImageFOMCalc
index 8e05814..a3982c9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/mrcImageFOMCalc and b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86MAC64/mrcImageFOMCalc differ

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/.Depend
index b538d85..d006421 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,69 +91,119 @@ mrcImageFOMCalc.o: mrcImageFOMCalc.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageFOMCalc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageFOMCalc.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFOMCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFOMCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFOMCalc.h

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/mrcImageFOMCalc b/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/mrcImageFOMCalc
index 8e05814..a3982c9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/mrcImageFOMCalc and b/src/Tools/mrcImage/mrcImageFOMCalc/src/X86MAC64/mrcImageFOMCalc differ

diff --git a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/.Depend
index 5eb3b7f..cb16db6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFeatureExtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFeatureExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFeatureExtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFeatureExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcImageFeatureExtraction.o: mrcImageFeatureExtraction.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFeatureExtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFeatureExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageFeatureExtraction.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageFeatureExtraction.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFeatureExtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFeatureExtraction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFeatureExtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFeatureExtraction.h

diff --git a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/mrcImageFeatureExtraction b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/mrcImageFeatureExtraction
index 1884377..f3b6bfc 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/mrcImageFeatureExtraction and b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86MAC64/mrcImageFeatureExtraction differ

diff --git a/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/.Depend
index 9531695..78092c4 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilamentSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilamentSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilamentSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilamentSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,54 +91,108 @@ mrcImageFilamentSearch.o: mrcImageFilamentSearch.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilamentSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilamentSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilamentSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilamentSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilamentSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilamentSearch.h

diff --git a/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFilamentSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/.Depend
index f402b76..5f02f2d 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilterCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilterCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilterCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilterCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,62 +91,114 @@ mrcImageFilterCreate.o: mrcImageFilterCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilterCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilterCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageFilterCreate.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageFilterCreate.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilterCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilterCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilterCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilterCreate.h

diff --git a/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/mrcImageFilterCreate b/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/mrcImageFilterCreate
index 7fd5b05..372f1a7 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/mrcImageFilterCreate and b/src/Tools/mrcImage/mrcImageFilterCreate/src/X86MAC64/mrcImageFilterCreate differ

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/.Depend
index 4e9d0be..605011c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageFilteringbyFile.o: mrcImageFilteringbyFile.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFile.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFile.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFile.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFile.h

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/mrcImageFilteringbyFile b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/mrcImageFilteringbyFile
index c0efe7e..930b666 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/mrcImageFilteringbyFile and b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86MAC64/mrcImageFilteringbyFile differ

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/.Depend
index e31d09e..655729b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/.Depend
@@ -4,28 +4,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFileForVariance.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFileForVariance.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -34,54 +48,85 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFileForVariance.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFileForVariance.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageFilteringbyFileForVariance.o:  \
- mrcImageFilteringbyFileForVariance.c /usr/include/stdio.h \
+mrcImageFilteringbyFileForVariance.o: \
+  mrcImageFilteringbyFileForVariance.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFileForVariance.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFileForVariance.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -92,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFileForVariance.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFileForVariance.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFilteringbyFileForVariance.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFilteringbyFileForVariance.h

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/mrcImageFilteringbyFileForVariance b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/mrcImageFilteringbyFileForVariance
index 0997eec..60308eb 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/mrcImageFilteringbyFileForVariance and b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86MAC64/mrcImageFilteringbyFileForVariance differ

diff --git a/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/.Depend
index 95e7542..d6b1845 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierPowerSpectrum.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierPowerSpectrum.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierPowerSpectrum.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierPowerSpectrum.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,20 +92,38 @@ mrcImageFourierPowerSpectrum.o: mrcImageFourierPowerSpectrum.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierPowerSpectrum.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierPowerSpectrum.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -89,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierPowerSpectrum.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierPowerSpectrum.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierPowerSpectrum.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierPowerSpectrum.h

diff --git a/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/.Depend
index 663ba16..eca32bb 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierShellCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierShellCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,71 +92,120 @@ mrcImageFourierShellCorrelation.o: mrcImageFourierShellCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierShellCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
-  /Applications/Eos.app/Eos/include/lmrcImageFourierShellCorrelation.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageFourierShellCorrelation.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierShellCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierShellCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFourierShellCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFourierShellCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/mrcImageFourierShellCorrelation b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/mrcImageFourierShellCorrelation
index 9867021..354fa11 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/mrcImageFourierShellCorrelation and b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86MAC64/mrcImageFourierShellCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/.Depend
index 0736493..7b95c53 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFractalFourierShellCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFractalFourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,65 +47,92 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFractalFourierShellCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFractalFourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageFractalFourierShellCorrelation.o:  \
- mrcImageFractalFourierShellCorrelation.c /usr/include/stdio.h \
+mrcImageFractalFourierShellCorrelation.o: \
+  mrcImageFractalFourierShellCorrelation.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageFractalFourierShellCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageFractalFourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageFourierShellCorrelation.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -100,34 +141,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFractalFourierShellCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFractalFourierShellCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageFractalFourierShellCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageFractalFourierShellCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/mrcImageFractalFourierShellCorrelation b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/mrcImageFractalFourierShellCorrelation
index 0b675b0..6979558 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/mrcImageFractalFourierShellCorrelation and b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86MAC64/mrcImageFractalFourierShellCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/.Depend
index 31d83d9..b4c8173 100644 (file)
--- a/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageFractalFrourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +48,87 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageFractalFrourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageFractalFrourierShellCorrelation.o:  \
- mrcImageFractalFrourierShellCorrelation.c /usr/include/stdio.h \
+mrcImageFractalFrourierShellCorrelation.o: \
+  mrcImageFractalFrourierShellCorrelation.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageFractalFrourierShellCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +138,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageFractalFrourierShellCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageFractalFrourierShellCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/.Depend
index f063838..6cbbef3 100644 (file)
--- a/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageGaussDisc.o: mrcImageGaussDisc.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageGaussDisc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageGaussDisc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussDisc.h

diff --git a/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/mrcImageGaussDisc b/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/mrcImageGaussDisc
index 60b1bf4..d8f6b6a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/mrcImageGaussDisc and b/src/Tools/mrcImage/mrcImageGaussDisc/src/X86MAC64/mrcImageGaussDisc differ

diff --git a/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/.Depend
index 82057d0..75be179 100644 (file)
--- a/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageGaussSphere.o: mrcImageGaussSphere.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageGaussSphere.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageGaussSphere.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageGaussSphere.h

diff --git a/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/mrcImageGaussSphere b/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/mrcImageGaussSphere
index fec993e..c89b109 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/mrcImageGaussSphere and b/src/Tools/mrcImage/mrcImageGaussSphere/src/X86MAC64/mrcImageGaussSphere differ

diff --git a/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/.Depend
index acc97e3..fdf5586 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHeaderChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHeaderChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHeaderChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHeaderChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageHeaderChange.o: mrcImageHeaderChange.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHeaderChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHeaderChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHeaderChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHeaderChange.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHeaderChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHeaderChange.h

diff --git a/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/mrcImageHeaderChange b/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/mrcImageHeaderChange
index fac6e1b..a87400c 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/mrcImageHeaderChange and b/src/Tools/mrcImage/mrcImageHeaderChange/src/X86MAC64/mrcImageHeaderChange differ

diff --git a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/.Depend
index 5e4db92..afac6f8 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalAveraging.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalAveraging.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalAveraging.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalAveraging.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageHelicalAveraging.o: mrcImageHelicalAveraging.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalAveraging.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalAveraging.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalAveraging.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalAveraging.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalAveraging.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalAveraging.h

diff --git a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/mrcImageHelicalAveraging b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/mrcImageHelicalAveraging
index 5769278..421797d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/mrcImageHelicalAveraging and b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86MAC64/mrcImageHelicalAveraging differ

diff --git a/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/.Depend
index 02977d6..fcb745c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalConvolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalConvolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalConvolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalConvolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageHelicalConvolution.o: mrcImageHelicalConvolution.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalConvolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalConvolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalConvolution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalConvolution.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalConvolution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalConvolution.h

diff --git a/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHelicalConvolution/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/.Depend
index 3cb435b..c713a1e 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageHelicalMappingFrom2DImage.o: mrcImageHelicalMappingFrom2DImage.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMappingFrom2DImage.h

diff --git a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/mrcImageHelicalMappingFrom2DImage b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/mrcImageHelicalMappingFrom2DImage
index b90cb3d..f82410e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/mrcImageHelicalMappingFrom2DImage and b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86MAC64/mrcImageHelicalMappingFrom2DImage differ

diff --git a/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/.Depend
index 06610a9..7f576c2 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMasking.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMasking.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMasking.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMasking.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageHelicalMasking.o: mrcImageHelicalMasking.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMasking.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMasking.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMasking.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMasking.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMasking.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMasking.h

diff --git a/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/mrcImageHelicalMasking b/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/mrcImageHelicalMasking
index 3d16030..5380697 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/mrcImageHelicalMasking and b/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86MAC64/mrcImageHelicalMasking differ

diff --git a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/.Depend
index fc6cb85..ab42dd2 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageHelicalMaskingBy2DImage.o: mrcImageHelicalMaskingBy2DImage.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalMaskingBy2DImage.h

diff --git a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/mrcImageHelicalMaskingBy2DImage b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/mrcImageHelicalMaskingBy2DImage
index 18833f0..6e0eb2e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/mrcImageHelicalMaskingBy2DImage and b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86MAC64/mrcImageHelicalMaskingBy2DImage differ

diff --git a/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/.Depend
index 0b8739a..cfd2b60 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageHelicalProjection.o: mrcImageHelicalProjection.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalProjection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHelicalProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHelicalProjection.h

diff --git a/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/mrcImageHelicalProjection b/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/mrcImageHelicalProjection
index 4100209..0f7479a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/mrcImageHelicalProjection and b/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86MAC64/mrcImageHelicalProjection differ

diff --git a/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/.Depend
index 3b8b469..b14af68 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,20 +91,38 @@ mrcImageHighPassFilter.o: mrcImageHighPassFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighPassFilter.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -88,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighPassFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighPassFilter.h

diff --git a/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/mrcImageHighPassFilter b/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/mrcImageHighPassFilter
index 66ab2d5..663706f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/mrcImageHighPassFilter and b/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86MAC64/mrcImageHighPassFilter differ

diff --git a/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/.Depend
index e2be096..5b560af 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighlighting.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighlighting.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighlighting.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighlighting.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,19 +91,38 @@ mrcImageHighlighting.o: mrcImageHighlighting.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  ../inc/config.h ../inc/../inc/mrcImageHighlighting.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h ../inc/config.h \
+  ../inc/../inc/mrcImageHighlighting.h \
   /Applications/Eos.app/Eos/include/mrcImage.h /usr/include/math.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -87,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighlighting.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighlighting.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageHighlighting.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageHighlighting.h

diff --git a/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/mrcImageHighlighting b/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/mrcImageHighlighting
new file mode 100755 (executable)
index 0000000..ee66543
Binary files /dev/null and b/src/Tools/mrcImage/mrcImageHighlighting/src/X86MAC64/mrcImageHighlighting differ

diff --git a/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/.Depend
index 01c1e6d..b82c5a5 100644 (file)
--- a/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,39 @@ mrcImageInfo.o: mrcImageInfo.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,32 +133,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageInfo.h

diff --git a/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/mrcImageInfo b/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/mrcImageInfo
index ed32f2a..7f7d0b0 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/mrcImageInfo and b/src/Tools/mrcImage/mrcImageInfo/src/X86MAC64/mrcImageInfo differ

diff --git a/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/.Depend
index a75e8c0..6a90669 100644 (file)
--- a/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageLabeling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageLabeling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageLabeling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageLabeling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageLabeling.o: mrcImageLabeling.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageLabeling.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageLabeling.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageLabeling.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageLabeling.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageLabeling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageLabeling.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageLabeling.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageLabeling.h

diff --git a/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/mrcImageLabeling b/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/mrcImageLabeling
index f233999..40a9ded 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/mrcImageLabeling and b/src/Tools/mrcImage/mrcImageLabeling/src/X86MAC64/mrcImageLabeling differ

diff --git a/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/.Depend
index 0539c53..cc3c077 100644 (file)
--- a/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageLowPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageLowPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageLowPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageLowPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,20 +91,38 @@ mrcImageLowPassFilter.o: mrcImageLowPassFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageLowPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageLowPassFilter.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -88,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageLowPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageLowPassFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageLowPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageLowPassFilter.h

diff --git a/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/mrcImageLowPassFilter b/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/mrcImageLowPassFilter
index f1f77ce..a028355 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/mrcImageLowPassFilter and b/src/Tools/mrcImage/mrcImageLowPassFilter/src/X86MAC64/mrcImageLowPassFilter differ

diff --git a/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/.Depend
index 4de5429..aa26bdc 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMagnificationChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMagnificationChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMagnificationChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMagnificationChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ lmrcImageMagnificationChange.o: lmrcImageMagnificationChange.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMagnificationChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMagnificationChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -92,23 +137,40 @@ mrcImageMagnificationChange.o: mrcImageMagnificationChange.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMagnificationChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMagnificationChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -119,34 +181,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMagnificationChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMagnificationChange.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMagnificationChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMagnificationChange.h

diff --git a/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/mrcImageMagnificationChange b/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/mrcImageMagnificationChange
index f8027fa..0b1833d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/mrcImageMagnificationChange and b/src/Tools/mrcImage/mrcImageMagnificationChange/src/X86MAC64/mrcImageMagnificationChange differ

diff --git a/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/.Depend
index b787b84..5ebf5ca 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMake2DArrayImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMake2DArrayImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMake2DArrayImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMake2DArrayImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageMake2DArrayImage.o: mrcImageMake2DArrayImage.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMake2DArrayImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMake2DArrayImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMake2DArrayImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMake2DArrayImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMake2DArrayImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMake2DArrayImage.h

diff --git a/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/mrcImageMake2DArrayImage b/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/mrcImageMake2DArrayImage
index 5d36435..355dd61 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/mrcImageMake2DArrayImage and b/src/Tools/mrcImage/mrcImageMake2DArrayImage/src/X86MAC64/mrcImageMake2DArrayImage differ

diff --git a/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/.Depend
index 97c1746..4b08297 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeCylinder.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeCylinder.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeCylinder.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeCylinder.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageMakeCylinder.o: mrcImageMakeCylinder.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeCylinder.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeCylinder.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeCylinder.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeCylinder.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeCylinder.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeCylinder.h

diff --git a/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/mrcImageMakeCylinder b/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/mrcImageMakeCylinder
index 48ac32f..6d40769 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/mrcImageMakeCylinder and b/src/Tools/mrcImage/mrcImageMakeCylinder/src/X86MAC64/mrcImageMakeCylinder differ

diff --git a/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/.Depend
index ba35c7f..c328652 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMakeDump.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeDump.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMakeDump.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeDump.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageMakeDump.o: mrcImageMakeDump.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMakeDump.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeDump.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeDump.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeDump.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeDump.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeDump.h

diff --git a/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/mrcImageMakeDump b/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/mrcImageMakeDump
index 95ab74e..93847e1 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/mrcImageMakeDump and b/src/Tools/mrcImage/mrcImageMakeDump/src/X86MAC64/mrcImageMakeDump differ

diff --git a/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/.Depend
index 5857acc..c6bbb3a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeFromTextFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeFromTextFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeFromTextFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeFromTextFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageMakeFromTextFile.o: mrcImageMakeFromTextFile.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeFromTextFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeFromTextFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeFromTextFile.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeFromTextFile.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeFromTextFile.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeFromTextFile.h

diff --git a/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/mrcImageMakeFromTextFile b/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/mrcImageMakeFromTextFile
index bafe3e7..50343df 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/mrcImageMakeFromTextFile and b/src/Tools/mrcImage/mrcImageMakeFromTextFile/src/X86MAC64/mrcImageMakeFromTextFile differ

diff --git a/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/.Depend
index 8b2a6e0..1e6d462 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageMakeSphere.o: mrcImageMakeSphere.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeSphere.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMakeSphere.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMakeSphere.h

diff --git a/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/mrcImageMakeSphere b/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/mrcImageMakeSphere
index c8bdaa4..2d0bcee 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/mrcImageMakeSphere and b/src/Tools/mrcImage/mrcImageMakeSphere/src/X86MAC64/mrcImageMakeSphere differ

diff --git a/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/.Depend
index bff5c4e..b6797bb 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMappingtoPdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMappingtoPdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMappingtoPdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMappingtoPdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,64 +91,115 @@ mrcImageMappingtoPdb.o: mrcImageMappingtoPdb.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMappingtoPdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMappingtoPdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/pdbInfoGet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMappingtoPdb.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMappingtoPdb.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMappingtoPdb.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMappingtoPdb.h

diff --git a/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/mrcImageMappingtoPdb b/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/mrcImageMappingtoPdb
index bf7d422..708af7d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/mrcImageMappingtoPdb and b/src/Tools/mrcImage/mrcImageMappingtoPdb/src/X86MAC64/mrcImageMappingtoPdb differ

diff --git a/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/.Depend
index d11b42a..95fc4c5 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMasking.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMasking.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMasking.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMasking.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,64 +91,115 @@ mrcImageMasking.o: mrcImageMasking.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMasking.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMasking.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/lmrcImageNormalizing.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/nr2.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMasking.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMasking.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMasking.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMasking.h

diff --git a/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/mrcImageMasking b/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/mrcImageMasking
index 8736bfe..e6d8421 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/mrcImageMasking and b/src/Tools/mrcImage/mrcImageMasking/src/X86MAC64/mrcImageMasking differ

diff --git a/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/.Depend
index 4832579..d013ce4 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMaskingByImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMaskingByImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMaskingByImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMaskingByImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageMaskingByImage.o: mrcImageMaskingByImage.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMaskingByImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMaskingByImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMaskingByImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMaskingByImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMaskingByImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMaskingByImage.h

diff --git a/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/mrcImageMaskingByImage b/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/mrcImageMaskingByImage
index bedd9f1..26eada2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/mrcImageMaskingByImage and b/src/Tools/mrcImage/mrcImageMaskingByImage/src/X86MAC64/mrcImageMaskingByImage differ

diff --git a/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/.Depend
index 88d18b9..1202413 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMergebyside.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMergebyside.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMergebyside.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMergebyside.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageMergebyside.o: mrcImageMergebyside.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMergebyside.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMergebyside.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMergebyside.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMergebyside.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMergebyside.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMergebyside.h

diff --git a/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/mrcImageMergebyside b/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/mrcImageMergebyside
index 6c22ba6..02a5cd2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/mrcImageMergebyside and b/src/Tools/mrcImage/mrcImageMergebyside/src/X86MAC64/mrcImageMergebyside differ

diff --git a/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/.Depend
index daf3805..1b459a6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMirroring.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMirroring.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMirroring.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMirroring.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageMirroring.o: mrcImageMirroring.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMirroring.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMirroring.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMirroring.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMirroring.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMirroring.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMirroring.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMirroring.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMirroring.h

diff --git a/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/mrcImageMirroring b/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/mrcImageMirroring
index 174b431..a625805 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/mrcImageMirroring and b/src/Tools/mrcImage/mrcImageMirroring/src/X86MAC64/mrcImageMirroring differ

diff --git a/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/.Depend
index 1823ff7..0d7493c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageModeChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModeChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageModeChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModeChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageModeChange.o: mrcImageModeChange.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageModeChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModeChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageModeChange.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageModeChange.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageModeChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageModeChange.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageModeChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageModeChange.h

diff --git a/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/mrcImageModeChange b/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/mrcImageModeChange
index b8d512b..bf98ff3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/mrcImageModeChange and b/src/Tools/mrcImage/mrcImageModeChange/src/X86MAC64/mrcImageModeChange differ

diff --git a/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/.Depend
index 11f5adf..3f4dfc3 100644 (file)
--- a/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageModelCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageModelCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageModelCreate.o: mrcImageModelCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageModelCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageModelCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageModelCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelCreate.h

diff --git a/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/mrcImageModelCreate b/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/mrcImageModelCreate
index 1a01d8a..b47a94b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/mrcImageModelCreate and b/src/Tools/mrcImage/mrcImageModelCreate/src/X86MAC64/mrcImageModelCreate differ

diff --git a/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/.Depend
index a477ab9..aa3fa3b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageModelSubfilamentsCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelSubfilamentsCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageModelSubfilamentsCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelSubfilamentsCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageModelSubfilamentsCreate.o: mrcImageModelSubfilamentsCreate.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageModelSubfilamentsCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelSubfilamentsCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageModelSubfilamentsCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelSubfilamentsCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageModelSubfilamentsCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageModelSubfilamentsCreate.h

diff --git a/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/mrcImageModelSubfilamentsCreate b/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/mrcImageModelSubfilamentsCreate
index 091785e..74e9013 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/mrcImageModelSubfilamentsCreate and b/src/Tools/mrcImage/mrcImageModelSubfilamentsCreate/src/X86MAC64/mrcImageModelSubfilamentsCreate differ

diff --git a/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/.Depend
index a0f1fc7..db3d099 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMontageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMontageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMontageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMontageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,35 +91,48 @@ mrcImageMontageCreate.o: mrcImageMontageCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMontageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMontageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageMontage.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImagePad.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -100,34 +141,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMontageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMontageCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMontageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMontageCreate.h

diff --git a/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/mrcImageMontageCreate b/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/mrcImageMontageCreate
index 5d8ed53..66369db 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/mrcImageMontageCreate and b/src/Tools/mrcImage/mrcImageMontageCreate/src/X86MAC64/mrcImageMontageCreate differ

diff --git a/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/.Depend
index 1940966..dbcd350 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,114 @@ mrcImageMove.o: mrcImageMove.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMove.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMove.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageMove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMove.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageMove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMove.h

diff --git a/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/mrcImageMove b/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/mrcImageMove
index be9d499..73ad73b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/mrcImageMove and b/src/Tools/mrcImage/mrcImageMove/src/X86MAC64/mrcImageMove differ

diff --git a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/.Depend
index acc2114..dc2dc21 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,73 +92,119 @@ mrcImageMultiCTFCompensation.o: mrcImageMultiCTFCompensation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFCompensation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFCompensation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lmrcImageCTFCompensation.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageCTFCompensation.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFCompensation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFCompensation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFCompensation.h

diff --git a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/mrcImageMultiCTFCompensation b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/mrcImageMultiCTFCompensation
index b08cdda..8bdb0a7 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/mrcImageMultiCTFCompensation and b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/mrcImageMultiCTFCompensation differ

diff --git a/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/.Depend
index 7c9f811..6dbce08 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFDetermination.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFDetermination.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFDetermination.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFDetermination.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,31 +92,45 @@ mrcImageMultiCTFDetermination.o: mrcImageMultiCTFDetermination.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFDetermination.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFDetermination.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -98,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFDetermination.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFDetermination.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiCTFDetermination.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiCTFDetermination.h

diff --git a/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/mrcImageMultiCTFDetermination b/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/mrcImageMultiCTFDetermination
index 469837f..4f8d9ce 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/mrcImageMultiCTFDetermination and b/src/Tools/mrcImage/mrcImageMultiCTFDetermination/src/X86MAC64/mrcImageMultiCTFDetermination differ

diff --git a/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/.Depend
index 15fdce9..b03dfb1 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMultiplying.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplying.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMultiplying.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplying.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,114 @@ mrcImageMultiplying.o: mrcImageMultiplying.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageMultiplying.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplying.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiplying.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplying.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiplying.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplying.h

diff --git a/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/mrcImageMultiplying b/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/mrcImageMultiplying
index c0a6fb2..3d3d1ea 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/mrcImageMultiplying and b/src/Tools/mrcImage/mrcImageMultiplying/src/X86MAC64/mrcImageMultiplying differ

diff --git a/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/.Depend
index 27f093e..23c70a7 100644 (file)
--- a/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiplyingbyFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplyingbyFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiplyingbyFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplyingbyFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageMultiplyingbyFile.o: mrcImageMultiplyingbyFile.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiplyingbyFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplyingbyFile.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiplyingbyFile.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplyingbyFile.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageMultiplyingbyFile.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageMultiplyingbyFile.h

diff --git a/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/mrcImageMultiplyingbyFile b/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/mrcImageMultiplyingbyFile
index 4c5f883..b68b8d7 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/mrcImageMultiplyingbyFile and b/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86MAC64/mrcImageMultiplyingbyFile differ

diff --git a/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/.Depend
index 25ac6a8..c64c78a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNLMeansFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNLMeansFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNLMeansFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNLMeansFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageNLMeansFilter.o: mrcImageNLMeansFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNLMeansFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNLMeansFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNLMeansFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNLMeansFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNLMeansFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNLMeansFilter.h

diff --git a/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/mrcImageNLMeansFilter b/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/mrcImageNLMeansFilter
index 3f53d4c..b50e6dc 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/mrcImageNLMeansFilter and b/src/Tools/mrcImage/mrcImageNLMeansFilter/src/X86MAC64/mrcImageNLMeansFilter differ

diff --git a/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/.Depend
index 7b24e7d..f1af309 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNfoldAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNfoldAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNfoldAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNfoldAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,63 +91,115 @@ mrcImageNfoldAxisSearch.o: mrcImageNfoldAxisSearch.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNfoldAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNfoldAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNfoldAxisSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNfoldAxisSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNfoldAxisSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNfoldAxisSearch.h

diff --git a/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/mrcImageNfoldAxisSearch b/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/mrcImageNfoldAxisSearch
index cf1ff5d..05a2325 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/mrcImageNfoldAxisSearch and b/src/Tools/mrcImage/mrcImageNfoldAxisSearch/src/X86MAC64/mrcImageNfoldAxisSearch differ

diff --git a/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/.Depend
index 9d6ec8f..960ef9f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,21 +91,43 @@ mrcImageNoiseAdd.o: mrcImageNoiseAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/mrcImage.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -86,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseAdd.h

diff --git a/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/mrcImageNoiseAdd b/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/mrcImageNoiseAdd
index 1930655..f8a65d4 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/mrcImageNoiseAdd and b/src/Tools/mrcImage/mrcImageNoiseAdd/src/X86MAC64/mrcImageNoiseAdd differ

diff --git a/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/.Depend
index f80072e..c4593b3 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,118 @@ mrcImageNoiseCreate.o: mrcImageNoiseCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseCreate.h

diff --git a/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/mrcImageNoiseCreate b/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/mrcImageNoiseCreate
index 900fc96..8af96c9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/mrcImageNoiseCreate and b/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86MAC64/mrcImageNoiseCreate differ

diff --git a/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/.Depend
index 92ababd..223cb8c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseReductionByRelaxation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseReductionByRelaxation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,56 +47,85 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseReductionByRelaxation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseReductionByRelaxation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageNoiseReductionByRelaxation.o:  \
- mrcImageNoiseReductionByRelaxation.c /usr/include/stdio.h \
+mrcImageNoiseReductionByRelaxation.o: \
+  mrcImageNoiseReductionByRelaxation.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseReductionByRelaxation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseReductionByRelaxation.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
@@ -92,57 +135,87 @@ mrcImageNoiseReductionByRelaxation.o:  \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lmrcImageSigmaCalculate.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageDataMaxAndMinGetByImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageDataStraightCopy.h \
   /Applications/Eos.app/Eos/include/lmrcImagePixelSummationOfProbabilityGetByImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageFirstNoiseReductionByRelaxation.h \
   /Applications/Eos.app/Eos/include/lmrcImageProportionalDensityLevelSetByImage.h \
-  /Applications/Eos.app/Eos/include/lmrcImageFirstNoiseReductionByRelaxation.h \
   /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxationRValueSet.h \
   /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxation.h \
   /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.h \
   /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.h \
   /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxationDijValueSet.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxationQValueSet.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxation.h
+  /Applications/Eos.app/Eos/include/lmrcImageSecondNoiseReductionByRelaxationQValueSet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseReductionByRelaxation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseReductionByRelaxation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNoiseReductionByRelaxation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNoiseReductionByRelaxation.h

diff --git a/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/mrcImageNoiseReductionByRelaxation b/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/mrcImageNoiseReductionByRelaxation
index 635f92e..bbfe999 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/mrcImageNoiseReductionByRelaxation and b/src/Tools/mrcImage/mrcImageNoiseReductionByRelaxation/src/X86MAC64/mrcImageNoiseReductionByRelaxation differ

diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/.Depend
index fa19402..295b3f6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNormalizedSubtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizedSubtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNormalizedSubtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizedSubtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,20 +92,38 @@ mrcImageNormalizedSubtraction.o: mrcImageNormalizedSubtraction.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNormalizedSubtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizedSubtraction.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,43 +131,77 @@ mrcImageNormalizedSubtraction.o: mrcImageNormalizedSubtraction.c \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageSubtractionCalc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageDensityNormalizationByImage.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSigmaCalculate.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
+  /Applications/Eos.app/Eos/include/lmrcImageSigmaCalculate.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNormalizedSubtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizedSubtraction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNormalizedSubtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizedSubtraction.h

diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction
index 89b1f82..16615e2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction and b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction differ

diff --git a/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/.Depend
index 80a82ad..844266b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNormalizing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNormalizing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,63 +91,115 @@ mrcImageNormalizing.o: mrcImageNormalizing.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageNormalizing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageNormalizing.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/nr2.h \
   /Applications/Eos.app/Eos/include/nr2.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNormalizing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNormalizing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNormalizing.h

diff --git a/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/mrcImageNormalizing b/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/mrcImageNormalizing
index f8c4118..08ec23e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/mrcImageNormalizing and b/src/Tools/mrcImage/mrcImageNormalizing/src/X86MAC64/mrcImageNormalizing differ

diff --git a/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/.Depend
index 08e5aa7..d4062a0 100644 (file)
--- a/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNullImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNullImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNullImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNullImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageNullImageCreate.o: mrcImageNullImageCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNullImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNullImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNullImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNullImageCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNullImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNullImageCreate.h

diff --git a/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/mrcImageNullImageCreate b/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/mrcImageNullImageCreate
index aa3c590..eff3836 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/mrcImageNullImageCreate and b/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86MAC64/mrcImageNullImageCreate differ

diff --git a/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/.Depend
index 9f64342..73ccb2d 100644 (file)
--- a/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,63 +91,116 @@ mrcImageOddBoxel.o: mrcImageOddBoxel.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/nr2.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOddBoxel.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOddBoxel.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOddBoxel.h

diff --git a/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/mrcImageOddBoxel b/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/mrcImageOddBoxel
index 3f30575..a6e4a85 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/mrcImageOddBoxel and b/src/Tools/mrcImage/mrcImageOddBoxel/src/X86MAC64/mrcImageOddBoxel differ

diff --git a/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/.Depend
index 2a816db..bd78322 100644 (file)
--- a/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageOneLineSimilarityCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOneLineSimilarityCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageOneLineSimilarityCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOneLineSimilarityCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcImageOneLineSimilarityCalc.o: mrcImageOneLineSimilarityCalc.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageOneLineSimilarityCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOneLineSimilarityCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageOneLineSimilarityCalc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageOneLineSimilarityCalc.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOneLineSimilarityCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOneLineSimilarityCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOneLineSimilarityCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOneLineSimilarityCalc.h

diff --git a/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/mrcImageOneLineSimilarityCalc b/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/mrcImageOneLineSimilarityCalc
index b2ce62e..814d3c5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/mrcImageOneLineSimilarityCalc and b/src/Tools/mrcImage/mrcImageOneLineSimilarityCalc/src/X86MAC64/mrcImageOneLineSimilarityCalc differ

diff --git a/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/.Depend
index b91ab89..3fbcb2b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageOpening.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOpening.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageOpening.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOpening.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageOpening.o: mrcImageOpening.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageOpening.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOpening.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMorphology.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOpening.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOpening.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOpening.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOpening.h

diff --git a/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/mrcImageOpening b/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/mrcImageOpening
index 8610daf..66eed8a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/mrcImageOpening and b/src/Tools/mrcImage/mrcImageOpening/src/X86MAC64/mrcImageOpening differ

diff --git a/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/.Depend
index 1e2bf8c..3d7a788 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/.Depend
@@ -3,228 +3,49 @@ mrcImagePCA.o: mrcImagePCA.cc /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
   /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/mrcImagePCA.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h ../inc/mrcImagePCA.h
-mrcImagePCA.o: mrcImagePCA.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/mrcImagePCA.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/mrcImagePCA.h
-mrcImagePCA.o: mrcImagePCA.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/mrcImagePCA.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
+  ../inc/../inc/mrcImagePCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/mrcImagePCA.h
-mrcImagePCA.o: mrcImagePCA.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/mrcImagePCA.h /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/mrcImagePCA.h
-mrcImagePCA.o: mrcImagePCA.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/mrcImagePCA.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/mrcImagePCA.h
-mrcImagePCA.o: mrcImagePCA.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/mrcImagePCA.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/mrcImagePCA.h
-mrcImagePCA.o: mrcImagePCA.cc /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
-  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/mrcImagePCA.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h ../inc/mrcImagePCA.h
+  /Applications/Eos.app/Eos/include/Array.h

diff --git a/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/mrcImagePCA b/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/mrcImagePCA
index 9a5a5ee..6ad459e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/mrcImagePCA and b/src/Tools/mrcImage/mrcImagePCA/src/X86MAC64/mrcImagePCA differ

diff --git a/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/.Depend
index d287263..6f776b3 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,68 +91,119 @@ mrcImagePad.o: mrcImagePad.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/lmrcImagePad.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/Memory.h
+  /Applications/Eos.app/Eos/include/lmrcImagePad.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImagePad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePad.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImagePad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePad.h

diff --git a/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/mrcImagePad b/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/mrcImagePad
index b1c4a78..83233c5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/mrcImagePad and b/src/Tools/mrcImage/mrcImagePad/src/X86MAC64/mrcImagePad differ

diff --git a/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/.Depend
new file mode 100644 (file)
index 0000000..f743328
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/.Depend
@@ -0,0 +1,208 @@
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePanoramaCreate.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
+  /usr/include/limits.h /usr/include/machine/limits.h \
+  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
+  /usr/include/sys/syslimits.h
+init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePanoramaCreate.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
+  /usr/include/limits.h /usr/include/machine/limits.h \
+  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
+  /usr/include/sys/syslimits.h
+mrcImagePanoramaCreate.o: mrcImagePanoramaCreate.c /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePanoramaCreate.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
+  /usr/include/limits.h /usr/include/machine/limits.h \
+  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Array.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePanoramaCreate.h
+util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePanoramaCreate.h

diff --git a/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/Makefile
new file mode 100755 (executable)
index 0000000..ec61247
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/Makefile
@@ -0,0 +1,114 @@
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineTool.inc
+
+LIBFILES   = \
+                       $(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+                       $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+                       $(OBJECTNAME).c \
+                       init.c \
+                       argCheck.c \
+                       usage.c  \
+                       util.c 
+
+SRCCXX  = \
+                       $(OBJECTNAME).cc \
+                       init.cc \
+                       argCheck.cc \
+                       usage.cc  \
+                       util.cc 
+
+MODULES    = \
+                       $(OBJECTNAME).o \
+                       init.o \
+                       argCheck.o \
+                       usage.o  \
+                       util.o 
+
+REALMODULES    = \
+                       $(OSTYPE)/$(OBJECTNAME).o \
+                       $(OSTYPE)/init.o \
+                       $(OSTYPE)/argCheck.o \
+                       $(OSTYPE)/usage.o \
+                       $(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+                       $(OBJECTNAME).debugo \
+                       init.debugo \
+                       argCheck.debugo \
+                       usage.debugo  \
+                       util.debugo 
+
+MODULESCUDAGDB    = \
+                       $(OBJECTNAME).cudagdb.o \
+                       init.cudagdb.o \
+                       argCheck.cudagdb.o \
+                       usage.cudagdb.o  \
+                       util.cudagdb.o 
+
+REALMODULESDEBUG    = \
+                       $(OSTYPE)/$(OBJECTNAME).debugo \
+                       $(OSTYPE)/init.debugo \
+                       $(OSTYPE)/argCheck.debugo \
+                       $(OSTYPE)/usage.debugo \
+                       $(OSTYPE)/util.debugo 
+
+
+$(OBJECTNAME): $(MODULES) $(LIBFILES)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+       fi
+
+
+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+
+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
+       echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
+       $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
+
+include ./.Depend
+include  $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/X86MAC64 b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/X86MAC64
new file mode 120000 (symlink)
index 0000000..b468c8c
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/X86MAC64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/mrcImagePanoramaCreate b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/mrcImagePanoramaCreate
new file mode 100755 (executable)
index 0000000..6f2d067
Binary files /dev/null and b/src/Tools/mrcImage/mrcImagePanoramaCreate/src/X86MAC64/mrcImagePanoramaCreate differ

diff --git a/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/.Depend
old mode 100755 (executable)
new mode 100644 (file)
index 16349f9..43362f5
--- a/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageParticleCandidateExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageParticleCandidateExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageParticleCandidateExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageParticleCandidateExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageParticleCandidateExtract.o: mrcImageParticleCandidateExtract.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageParticleCandidateExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageParticleCandidateExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageParticleCandidateExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageParticleCandidateExtract.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageParticleCandidateExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageParticleCandidateExtract.h

diff --git a/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/mrcImageParticleCandidateExtract b/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/mrcImageParticleCandidateExtract
index 4d8519e..3bf7e7d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/mrcImageParticleCandidateExtract and b/src/Tools/mrcImage/mrcImageParticleCandidateExtract/src/X86MAC64/mrcImageParticleCandidateExtract differ

diff --git a/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/.Depend
index 9f56b40..a801738 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,115 @@ mrcImagePeakSearch.o: mrcImagePeakSearch.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageBinarization.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageCalcArea.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePeakSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePeakSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePeakSearch.h

diff --git a/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/mrcImagePeakSearch b/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/mrcImagePeakSearch
index f57f30d..087aeec 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/mrcImagePeakSearch and b/src/Tools/mrcImage/mrcImagePeakSearch/src/X86MAC64/mrcImagePeakSearch differ

diff --git a/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/.Depend
index 0c00697..6457be9 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImagePhaseCTFCompensationFromCTFINFO.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +48,87 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImagePhaseCTFCompensationFromCTFINFO.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImagePhaseCTFCompensationFromCTFINFO.o:  \
- mrcImagePhaseCTFCompensationFromCTFINFO.c /usr/include/stdio.h \
+mrcImagePhaseCTFCompensationFromCTFINFO.o: \
+  mrcImagePhaseCTFCompensationFromCTFINFO.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImagePhaseCTFCompensationFromCTFINFO.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +138,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImagePhaseCTFCompensationFromCTFINFO.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImagePhaseCTFCompensationFromCTFINFO.h

diff --git a/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO b/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO
index 1428620..a133bbf 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO and b/src/Tools/mrcImage/mrcImagePhaseCTFCompensationFromCTFINFO/src/X86MAC64/mrcImagePhaseCTFCompensationFromCTFINFO differ

diff --git a/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/.Depend
index 557c1e9..e31db73 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagePixelDataGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePixelDataGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagePixelDataGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePixelDataGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImagePixelDataGet.o: mrcImagePixelDataGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagePixelDataGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePixelDataGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePixelDataGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePixelDataGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePixelDataGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePixelDataGet.h

diff --git a/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/mrcImagePixelDataGet b/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/mrcImagePixelDataGet
index 56e8df3..b3dc77a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/mrcImagePixelDataGet and b/src/Tools/mrcImage/mrcImagePixelDataGet/src/X86MAC64/mrcImagePixelDataGet differ

diff --git a/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/.Depend
index 4bddf36..cca75c1 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePolyROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePolyROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePolyROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePolyROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImagePolyROI.o: mrcImagePolyROI.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePolyROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePolyROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePolyROI.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePolyROI.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePolyROI.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePolyROI.h

diff --git a/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/mrcImagePolyROI b/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/mrcImagePolyROI
index 5426a9e..09c3847 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/mrcImagePolyROI and b/src/Tools/mrcImage/mrcImagePolyROI/src/X86MAC64/mrcImagePolyROI differ

diff --git a/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/.Depend
index 8107ce2..fd8e8cf 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagePosterization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePosterization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagePosterization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePosterization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,62 +91,114 @@ mrcImagePosterization.o: mrcImagePosterization.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagePosterization.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePosterization.h \
   /Applications/Eos.app/Eos/include/lmrcImagePosterization.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/Array.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePosterization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePosterization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePosterization.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePosterization.h

diff --git a/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/mrcImagePosterization b/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/mrcImagePosterization
index 0f1f6c1..33401e3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/mrcImagePosterization and b/src/Tools/mrcImage/mrcImagePosterization/src/X86MAC64/mrcImagePosterization differ

diff --git a/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/.Depend
index 5e174fc..5b216a1 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,37 @@ mrcImagePrint.o: mrcImagePrint.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagePrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePrint.h \
   /Applications/Eos.app/Eos/include/lmrcImagePrint.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
@@ -83,12 +131,8 @@ mrcImagePrint.o: mrcImagePrint.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/psFile.h \
   /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -97,34 +141,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePrint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePrint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint.h

diff --git a/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/mrcImagePrint b/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/mrcImagePrint
index 7489ff1..e64030f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/mrcImagePrint and b/src/Tools/mrcImage/mrcImagePrint/src/X86MAC64/mrcImagePrint differ

diff --git a/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/.Depend
index f4b0912..5abbf22 100644 (file)
--- a/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePrint3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePrint3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,52 +91,107 @@ mrcImagePrint3D.o: mrcImagePrint3D.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagePrint3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint3D.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePrint3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint3D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagePrint3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagePrint3D.h

diff --git a/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/mrcImagePrint3D b/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/mrcImagePrint3D
index 4383f44..cd771fc 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/mrcImagePrint3D and b/src/Tools/mrcImage/mrcImagePrint3D/src/X86MAC64/mrcImagePrint3D differ

diff --git a/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/.Depend
index 74ced6f..88baa7c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,114 @@ mrcImageProjection.o: mrcImageProjection.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageProjection.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageProjection.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageProjection.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageProjection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageProjection.h

diff --git a/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/mrcImageProjection b/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/mrcImageProjection
index cf60adc..a78125b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/mrcImageProjection and b/src/Tools/mrcImage/mrcImageProjection/src/X86MAC64/mrcImageProjection differ

diff --git a/src/Tools/mrcImage/mrcImagePut3D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagePut3D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagePut3D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagePut3D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/.Depend
index 8cb8dba..43ad384 100644 (file)
--- a/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,114 @@ mrcImageROI.o: mrcImageROI.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageROI2D.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageROI2D.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageROI.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageROI.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI.h

diff --git a/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/mrcImageROI b/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/mrcImageROI
index e6e4c3b..c750e50 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/mrcImageROI and b/src/Tools/mrcImage/mrcImageROI/src/X86MAC64/mrcImageROI differ

diff --git a/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/.Depend
index f8afc22..1b1fda1 100644 (file)
--- a/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROI3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROI3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageROI3D.o: mrcImageROI3D.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROI3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI3D.h \
   /Applications/Eos.app/Eos/include/lmrcImageROI3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
@@ -86,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageROI3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI3D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageROI3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROI3D.h

diff --git a/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/mrcImageROI3D b/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/mrcImageROI3D
index de83a99..9330219 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/mrcImageROI3D and b/src/Tools/mrcImage/mrcImageROI3D/src/X86MAC64/mrcImageROI3D differ

diff --git a/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/.Depend
index ef02bff..724198f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROIs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROIs.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROIs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROIs.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,71 +91,121 @@ mrcImageROIs.o: mrcImageROIs.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageROIs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROIs.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageROI2D.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageMontage.h \
-  /Applications/Eos.app/Eos/include/lmrcImagePad.h \
-  /Applications/Eos.app/Eos/include/Memory.h
+  /Applications/Eos.app/Eos/include/lmrcImagePad.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageROIs.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROIs.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageROIs.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROIs.h

diff --git a/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/mrcImageROIs b/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/mrcImageROIs
index b82ee3b..7cb7440 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/mrcImageROIs and b/src/Tools/mrcImage/mrcImageROIs/src/X86MAC64/mrcImageROIs differ

diff --git a/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/.Depend
index 695c176..29574a3 100644 (file)
--- a/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageROItoPCAoutputImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROItoPCAoutputImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageROItoPCAoutputImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageROItoPCAoutputImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,32 +92,49 @@ mrcImageROItoPCAoutputImage.o: mrcImageROItoPCAoutputImage.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
   /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
   ../inc/../inc/mrcImageROItoPCAoutputImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h ../inc/mrcImageROItoPCAoutputImage.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -99,34 +144,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageROItoPCAoutputImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROItoPCAoutputImage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageROItoPCAoutputImage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageROItoPCAoutputImage.h

diff --git a/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/mrcImageROItoPCAoutputImage b/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/mrcImageROItoPCAoutputImage
index 53140d4..37abe69 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/mrcImageROItoPCAoutputImage and b/src/Tools/mrcImage/mrcImageROItoPCAoutputImage/src/X86MAC64/mrcImageROItoPCAoutputImage differ

diff --git a/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/.Depend
index 94d24ae..1b5919a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadialDistribution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadialDistribution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadialDistribution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadialDistribution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,74 +92,122 @@ mrcImageRadialDistribution.o: mrcImageRadialDistribution.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadialDistribution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadialDistribution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageRadialDistribution.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageDensityInverse.h \
   /Applications/Eos.app/Eos/include/lmrcImageDensity.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/lmrcImageModeChange.h \
-  /Applications/Eos.app/Eos/include/Vector.h
+  /Applications/Eos.app/Eos/include/lmrcImageModeChange.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadialDistribution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadialDistribution.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadialDistribution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadialDistribution.h

diff --git a/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/mrcImageRadialDistribution b/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/mrcImageRadialDistribution
index 4755cba..71b2ae4 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/mrcImageRadialDistribution and b/src/Tools/mrcImage/mrcImageRadialDistribution/src/X86MAC64/mrcImageRadialDistribution differ

diff --git a/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/.Depend
index e6a309c..5dee26b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRandomParticlesImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRandomParticlesImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,62 +47,90 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRandomParticlesImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRandomParticlesImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageRandomParticlesImageCreate.o:  \
- mrcImageRandomParticlesImageCreate.c /usr/include/stdio.h \
+mrcImageRandomParticlesImageCreate.o: \
+  mrcImageRandomParticlesImageCreate.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRandomParticlesImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRandomParticlesImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -98,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRandomParticlesImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRandomParticlesImageCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRandomParticlesImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRandomParticlesImageCreate.h

diff --git a/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/mrcImageRandomParticlesImageCreate b/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/mrcImageRandomParticlesImageCreate
index 53a836f..c3b652d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/mrcImageRandomParticlesImageCreate and b/src/Tools/mrcImage/mrcImageRandomParticlesImageCreate/src/X86MAC64/mrcImageRandomParticlesImageCreate differ

diff --git a/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/.Depend
index 078207b..2a8ce11 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRealValueAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRealValueAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRealValueAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRealValueAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageRealValueAdd.o: mrcImageRealValueAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRealValueAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRealValueAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRealValueAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRealValueAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRealValueAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRealValueAdd.h

diff --git a/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/mrcImageRealValueAdd b/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/mrcImageRealValueAdd
index 96c1864..6e4219b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/mrcImageRealValueAdd and b/src/Tools/mrcImage/mrcImageRealValueAdd/src/X86MAC64/mrcImageRealValueAdd differ

diff --git a/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/.Depend
index db92d71..fe941cb 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageRectangleGet.o: mrcImageRectangleGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGet.h

diff --git a/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/mrcImageRectangleGet b/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/mrcImageRectangleGet
index 91c8fc6..73cf380 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/mrcImageRectangleGet and b/src/Tools/mrcImage/mrcImageRectangleGet/src/X86MAC64/mrcImageRectangleGet differ

diff --git a/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/.Depend
index f44eade..6e1e448 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGetByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGetByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGetByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGetByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageRectangleGetByCorrelation.o: mrcImageRectangleGetByCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGetByCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGetByCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGetByCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGetByCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRectangleGetByCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRectangleGetByCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/mrcImageRectangleGetByCorrelation b/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/mrcImageRectangleGetByCorrelation
index 6ac9fd6..dce20f3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/mrcImageRectangleGetByCorrelation and b/src/Tools/mrcImage/mrcImageRectangleGetByCorrelation/src/X86MAC64/mrcImageRectangleGetByCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/.Depend
index e4ef632..1be5f52 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageRefConv2D.o: mrcImageRefConv2D.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefConv2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefConv2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefConv2D.h

diff --git a/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/mrcImageRefConv2D b/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/mrcImageRefConv2D
index 1045f0c..4f4c629 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/mrcImageRefConv2D and b/src/Tools/mrcImage/mrcImageRefConv2D/src/X86MAC64/mrcImageRefConv2D differ

diff --git a/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/.Depend
index 98da599..e986d19 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRefCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRefCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageRefCreate.o: mrcImageRefCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRefCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefCreate.h

diff --git a/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/mrcImageRefCreate b/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/mrcImageRefCreate
index 73fc1db..9d656d0 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/mrcImageRefCreate and b/src/Tools/mrcImage/mrcImageRefCreate/src/X86MAC64/mrcImageRefCreate differ

diff --git a/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/.Depend
index 58f4c37..e6c20c6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefFFTConv2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefFFTConv2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefFFTConv2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefFFTConv2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageRefFFTConv2D.o: mrcImageRefFFTConv2D.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefFFTConv2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefFFTConv2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefFFTConv2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefFFTConv2D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefFFTConv2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefFFTConv2D.h

diff --git a/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/mrcImageRefFFTConv2D b/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/mrcImageRefFFTConv2D
index fa98f5a..27c2107 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/mrcImageRefFFTConv2D and b/src/Tools/mrcImage/mrcImageRefFFTConv2D/src/X86MAC64/mrcImageRefFFTConv2D differ

diff --git a/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/.Depend
index 8c5c77b..c1152e7 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefScaleChangeWithPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefScaleChangeWithPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefScaleChangeWithPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefScaleChangeWithPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageRefScaleChangeWithPad.o: mrcImageRefScaleChangeWithPad.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefScaleChangeWithPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefScaleChangeWithPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefScaleChangeWithPad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefScaleChangeWithPad.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRefScaleChangeWithPad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRefScaleChangeWithPad.h

diff --git a/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/mrcImageRefScaleChangeWithPad b/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/mrcImageRefScaleChangeWithPad
index 98c13e6..e31b9b9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/mrcImageRefScaleChangeWithPad and b/src/Tools/mrcImage/mrcImageRefScaleChangeWithPad/src/X86MAC64/mrcImageRefScaleChangeWithPad differ

diff --git a/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/.Depend
index 0b857b6..7c80245 100644 (file)
--- a/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageResolutionEstimateForFilaments.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageResolutionEstimateForFilaments.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +47,85 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageResolutionEstimateForFilaments.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageResolutionEstimateForFilaments.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageResolutionEstimateForFilaments.o:  \
- mrcImageResolutionEstimateForFilaments.c /usr/include/stdio.h \
+mrcImageResolutionEstimateForFilaments.o: \
+  mrcImageResolutionEstimateForFilaments.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageResolutionEstimateForFilaments.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageResolutionEstimateForFilaments.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageResolutionEstimateForFilaments.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageResolutionEstimateForFilaments.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageResolutionEstimateForFilaments.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageResolutionEstimateForFilaments.h

diff --git a/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/mrcImageResolutionEstimateForFilaments b/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/mrcImageResolutionEstimateForFilaments
index 38649f3..527c5fa 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/mrcImageResolutionEstimateForFilaments and b/src/Tools/mrcImage/mrcImageResolutionEstimateForFilaments/src/X86MAC64/mrcImageResolutionEstimateForFilaments differ

diff --git a/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/.Depend
index ea02c24..9a9908b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageReverse.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageReverse.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageReverse.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageReverse.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageReverse.o: mrcImageReverse.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageReverse.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageReverse.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageReverse.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageReverse.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageReverse.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageReverse.h

diff --git a/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/mrcImageReverse b/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/mrcImageReverse
index f67b720..6ee73a3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/mrcImageReverse and b/src/Tools/mrcImage/mrcImageReverse/src/X86MAC64/mrcImageReverse differ

diff --git a/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/.Depend
index 0573bba..d71a744 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageRotation.o: mrcImageRotation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation.h

diff --git a/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/mrcImageRotation b/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/mrcImageRotation
index faabd15..d0b420e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/mrcImageRotation and b/src/Tools/mrcImage/mrcImageRotation/src/X86MAC64/mrcImageRotation differ

diff --git a/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/.Depend
index a68f4e5..353c724 100644 (file)
--- a/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRotation3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRotation3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageRotation3D.o: mrcImageRotation3D.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageRotation3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRotation3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation3D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRotation3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRotation3D.h

diff --git a/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/mrcImageRotation3D b/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/mrcImageRotation3D
index 3850450..8aa0ea8 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/mrcImageRotation3D and b/src/Tools/mrcImage/mrcImageRotation3D/src/X86MAC64/mrcImageRotation3D differ

diff --git a/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/.Depend
index 9ff3135..3ee4ad6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSN.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSN.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,24 +91,40 @@ mrcImageSN.o: mrcImageSN.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSN.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSN.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
@@ -94,32 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageSN.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSN.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageSN.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSN.h

diff --git a/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/mrcImageSN b/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/mrcImageSN
index 72fa2a2..9a19605 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/mrcImageSN and b/src/Tools/mrcImage/mrcImageSN/src/X86MAC64/mrcImageSN differ

diff --git a/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/.Depend
index c978f6d..b0af1b6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSamplingUnitChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSamplingUnitChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSamplingUnitChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSamplingUnitChange.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,61 +92,114 @@ mrcImageSamplingUnitChange.o: mrcImageSamplingUnitChange.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSamplingUnitChange.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSamplingUnitChange.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSamplingUnitChange.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageSamplingUnitChange.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSamplingUnitChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSamplingUnitChange.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSamplingUnitChange.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSamplingUnitChange.h

diff --git a/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/mrcImageSamplingUnitChange b/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/mrcImageSamplingUnitChange
index f399236..af9dd88 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/mrcImageSamplingUnitChange and b/src/Tools/mrcImage/mrcImageSamplingUnitChange/src/X86MAC64/mrcImageSamplingUnitChange differ

diff --git a/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/.Depend
index 2c0ad86..50d3bbb 100644 (file)
--- a/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageScalarAdd.o: mrcImageScalarAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageScalarAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageScalarAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageScalarAdd.h

diff --git a/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/mrcImageScalarAdd b/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/mrcImageScalarAdd
index 3cce663..9e4510e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/mrcImageScalarAdd and b/src/Tools/mrcImage/mrcImageScalarAdd/src/X86MAC64/mrcImageScalarAdd differ

diff --git a/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/.Depend
index b16208d..2d86641 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSectionGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSectionGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSectionGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSectionGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageSectionGet.o: mrcImageSectionGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSectionGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSectionGet.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSectionGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSectionGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSectionGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSectionGet.h

diff --git a/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/mrcImageSectionGet b/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/mrcImageSectionGet
index 0779c91..c35d9c3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/mrcImageSectionGet and b/src/Tools/mrcImage/mrcImageSectionGet/src/X86MAC64/mrcImageSectionGet differ

diff --git a/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/.Depend
index 2f76e27..7020374 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSetFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSetFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSetFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSetFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageSetFunction.o: mrcImageSetFunction.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSetFunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSetFunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSetFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSetFunction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSetFunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSetFunction.h

diff --git a/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/mrcImageSetFunction b/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/mrcImageSetFunction
index 5091aa4..5ece301 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/mrcImageSetFunction and b/src/Tools/mrcImage/mrcImageSetFunction/src/X86MAC64/mrcImageSetFunction differ

diff --git a/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/.Depend
new file mode 100644 (file)
index 0000000..847f1b1
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/.Depend
@@ -0,0 +1,204 @@
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapeOrientation.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
+  /usr/include/limits.h /usr/include/machine/limits.h \
+  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
+  /usr/include/sys/syslimits.h
+init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapeOrientation.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
+  /usr/include/limits.h /usr/include/machine/limits.h \
+  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
+  /usr/include/sys/syslimits.h
+mrcImageShapeOrientation.o: mrcImageShapeOrientation.c \
+  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapeOrientation.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Array.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapeOrientation.h
+util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapeOrientation.h

diff --git a/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/Makefile
new file mode 100755 (executable)
index 0000000..ec61247
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/Makefile
@@ -0,0 +1,114 @@
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineTool.inc
+
+LIBFILES   = \
+                       $(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+                       $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+                       $(OBJECTNAME).c \
+                       init.c \
+                       argCheck.c \
+                       usage.c  \
+                       util.c 
+
+SRCCXX  = \
+                       $(OBJECTNAME).cc \
+                       init.cc \
+                       argCheck.cc \
+                       usage.cc  \
+                       util.cc 
+
+MODULES    = \
+                       $(OBJECTNAME).o \
+                       init.o \
+                       argCheck.o \
+                       usage.o  \
+                       util.o 
+
+REALMODULES    = \
+                       $(OSTYPE)/$(OBJECTNAME).o \
+                       $(OSTYPE)/init.o \
+                       $(OSTYPE)/argCheck.o \
+                       $(OSTYPE)/usage.o \
+                       $(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+                       $(OBJECTNAME).debugo \
+                       init.debugo \
+                       argCheck.debugo \
+                       usage.debugo  \
+                       util.debugo 
+
+MODULESCUDAGDB    = \
+                       $(OBJECTNAME).cudagdb.o \
+                       init.cudagdb.o \
+                       argCheck.cudagdb.o \
+                       usage.cudagdb.o  \
+                       util.cudagdb.o 
+
+REALMODULESDEBUG    = \
+                       $(OSTYPE)/$(OBJECTNAME).debugo \
+                       $(OSTYPE)/init.debugo \
+                       $(OSTYPE)/argCheck.debugo \
+                       $(OSTYPE)/usage.debugo \
+                       $(OSTYPE)/util.debugo 
+
+
+$(OBJECTNAME): $(MODULES) $(LIBFILES)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+       fi
+
+
+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+
+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
+       echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
+       $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
+
+include ./.Depend
+include  $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/X86MAC64 b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/X86MAC64
new file mode 120000 (symlink)
index 0000000..dabaa6d
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/X86MAC64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/mrcImageShapeOrientation b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/mrcImageShapeOrientation
new file mode 100755 (executable)
index 0000000..1dec128
Binary files /dev/null and b/src/Tools/mrcImage/mrcImageShapeOrientation/src/X86MAC64/mrcImageShapeOrientation differ

diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/.Depend
index 140efe1..b67394c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShapePCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShapePCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,114 @@ mrcImageShapePCA.o: mrcImageShapePCA.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShapePCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageShapePCA.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageShapePCA.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShapePCA.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCA.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShapePCA.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCA.h

diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA b/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA
index 1d3d544..4467bb3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA and b/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA differ

diff --git a/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/.Depend
index a2bced3..b15756f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageShapePCAFit.o: mrcImageShapePCAFit.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageShapePCA.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageShapePCA.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShapePCAFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShapePCAFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShapePCAFit.h

diff --git a/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/mrcImageShapePCAFit b/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/mrcImageShapePCAFit
index dcdee69..e57ab50 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/mrcImageShapePCAFit and b/src/Tools/mrcImage/mrcImageShapePCAFit/src/X86MAC64/mrcImageShapePCAFit differ

diff --git a/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/.Depend
index 2055dd2..e9dd754 100644 (file)
--- a/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShift.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShift.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShift.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShift.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageShift.o: mrcImageShift.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShift.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShift.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShift.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShift.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShift.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShift.h

diff --git a/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/mrcImageShift b/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/mrcImageShift
index 822cae9..a965af6 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/mrcImageShift and b/src/Tools/mrcImage/mrcImageShift/src/X86MAC64/mrcImageShift differ

diff --git a/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/.Depend
index fd51ef0..776425c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageShiftFollowingGC.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShiftFollowingGC.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageShiftFollowingGC.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShiftFollowingGC.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,37 +92,50 @@ mrcImageShiftFollowingGC.o: mrcImageShiftFollowingGC.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageShiftFollowingGC.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShiftFollowingGC.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageDensity.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageModeChange.h \
   /Applications/Eos.app/Eos/include/lmrcImageDensityInverse.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -102,34 +143,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShiftFollowingGC.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShiftFollowingGC.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShiftFollowingGC.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShiftFollowingGC.h

diff --git a/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/mrcImageShiftFollowingGC b/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/mrcImageShiftFollowingGC
index 392b9ec..9524e23 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/mrcImageShiftFollowingGC and b/src/Tools/mrcImage/mrcImageShiftFollowingGC/src/X86MAC64/mrcImageShiftFollowingGC differ

diff --git a/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/.Depend
index 5646dd3..51f235a 100644 (file)
--- a/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShrink.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShrink.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShrink.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShrink.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageShrink.o: mrcImageShrink.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageShrink.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageShrink.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShrink.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShrink.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageShrink.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageShrink.h

diff --git a/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/mrcImageShrink b/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/mrcImageShrink
index 0e4d7b8..243fbf6 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/mrcImageShrink and b/src/Tools/mrcImage/mrcImageShrink/src/X86MAC64/mrcImageShrink differ

diff --git a/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/.Depend
index f61cfb2..0af0527 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageSiemensStar.o: mrcImageSiemensStar.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSiemensStar.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSiemensStar.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSiemensStar.h

diff --git a/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/mrcImageSiemensStar b/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/mrcImageSiemensStar
index 190dd7f..ee9ba69 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/mrcImageSiemensStar and b/src/Tools/mrcImage/mrcImageSiemensStar/src/X86MAC64/mrcImageSiemensStar differ

diff --git a/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/.Depend
index a8aea52..5161dd7 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarImageSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarImageSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarImageSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarImageSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageSimilarImageSearch.o: mrcImageSimilarImageSearch.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarImageSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarImageSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarImageSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarImageSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarImageSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarImageSearch.h

diff --git a/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/mrcImageSimilarImageSearch b/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/mrcImageSimilarImageSearch
index 5426a9e..09c3847 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/mrcImageSimilarImageSearch and b/src/Tools/mrcImage/mrcImageSimilarImageSearch/src/X86MAC64/mrcImageSimilarImageSearch differ

diff --git a/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/.Depend
index e198e17..889d7dc 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarityEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarityEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarityEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarityEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,74 +92,121 @@ mrcImageSimilarityEstimate.o: mrcImageSimilarityEstimate.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarityEstimate.h \
-  /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarityEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageCorrelation.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/PVM.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSSDA.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h
+  /Applications/Eos.app/Eos/include/lmrcImageSSDA.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarityEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarityEstimate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSimilarityEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSimilarityEstimate.h

diff --git a/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/mrcImageSimilarityEstimate b/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/mrcImageSimilarityEstimate
index 1238b51..cd45a67 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/mrcImageSimilarityEstimate and b/src/Tools/mrcImage/mrcImageSimilarityEstimate/src/X86MAC64/mrcImageSimilarityEstimate differ

diff --git a/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/.Depend
index 0ef47f7..23b055c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcImageSinogramCorrelation.o: mrcImageSinogramCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSinogram.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageSinogram.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/mrcImageSinogramCorrelation b/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/mrcImageSinogramCorrelation
index 86e855a..5211598 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/mrcImageSinogramCorrelation and b/src/Tools/mrcImage/mrcImageSinogramCorrelation/src/X86MAC64/mrcImageSinogramCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/.Depend
index 09eb3e9..20e5b83 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,62 +91,114 @@ mrcImageSinogramCreate.o: mrcImageSinogramCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSinogram.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageSinogram.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramCreate.h

diff --git a/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/mrcImageSinogramCreate b/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/mrcImageSinogramCreate
index 7956a86..5b89a3d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/mrcImageSinogramCreate and b/src/Tools/mrcImage/mrcImageSinogramCreate/src/X86MAC64/mrcImageSinogramCreate differ

diff --git a/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/.Depend
index e3615c9..470e21e 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageSinogramFFT.o: mrcImageSinogramFFT.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramFFT.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSinogramFFT.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSinogramFFT.h

diff --git a/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/mrcImageSinogramFFT b/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/mrcImageSinogramFFT
index ab6f20f..2a943a7 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/mrcImageSinogramFFT and b/src/Tools/mrcImage/mrcImageSinogramFFT/src/X86MAC64/mrcImageSinogramFFT differ

diff --git a/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/.Depend
index b5fab24..851f506 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,113 @@ mrcImageSmoothing.o: mrcImageSmoothing.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSmoothing.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
+  /Applications/Eos.app/Eos/include/Array.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSmoothing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSmoothing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSmoothing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSmoothing.h

diff --git a/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/mrcImageSmoothing b/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/mrcImageSmoothing
index 16a5b74..714b217 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/mrcImageSmoothing and b/src/Tools/mrcImage/mrcImageSmoothing/src/X86MAC64/mrcImageSmoothing differ

diff --git a/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/.Depend
index 185ec8c..28b773c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSolventFlattening.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSolventFlattening.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSolventFlattening.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSolventFlattening.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,20 +92,38 @@ mrcImageSolventFlattening.o: mrcImageSolventFlattening.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSolventFlattening.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSolventFlattening.h \
   /Applications/Eos.app/Eos/include/lmrcImageSolventFlattening.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
@@ -90,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSolventFlattening.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSolventFlattening.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSolventFlattening.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSolventFlattening.h

diff --git a/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/mrcImageSolventFlattening b/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/mrcImageSolventFlattening
index 08340fd..2c8098a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/mrcImageSolventFlattening and b/src/Tools/mrcImage/mrcImageSolventFlattening/src/X86MAC64/mrcImageSolventFlattening differ

diff --git a/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/.Depend
index ddd721e..81d8d91 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageSphere.o: mrcImageSphere.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSphere.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphere.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSphere.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageSphere.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSphere.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphere.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSphere.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphere.h

diff --git a/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/mrcImageSphere b/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/mrcImageSphere
index 8777cd2..3fd198a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/mrcImageSphere and b/src/Tools/mrcImage/mrcImageSphere/src/X86MAC64/mrcImageSphere differ

diff --git a/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/.Depend
index ecf52c4..ac47a12 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageSphereCheck.o: mrcImageSphereCheck.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSphereCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSphereCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSphereCheck.h

diff --git a/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSphereCheck/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/.Depend
index bfab670..6e3b6ff 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSplit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSplit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSplit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSplit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageSplit.o: mrcImageSplit.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSplit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSplit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSplit.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageSplit.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSplit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSplit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSplit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSplit.h

diff --git a/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/mrcImageSplit b/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/mrcImageSplit
index f66f042..463aa35 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/mrcImageSplit and b/src/Tools/mrcImage/mrcImageSplit/src/X86MAC64/mrcImageSplit differ

diff --git a/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/.Depend
index 3cc959e..09f484d 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSquare.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSquare.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSquare.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSquare.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageSquare.o: mrcImageSquare.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSquare.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSquare.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSquare.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSquare.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSquare.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSquare.h

diff --git a/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/mrcImageSquare b/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/mrcImageSquare
index 789bea2..4050498 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/mrcImageSquare and b/src/Tools/mrcImage/mrcImageSquare/src/X86MAC64/mrcImageSquare differ

diff --git a/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/.Depend
index 9aa100f..83628f1 100644 (file)
--- a/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageStack.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageStack.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageStack.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageStack.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageStack.o: mrcImageStack.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageStack.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageStack.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageStack.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageStack.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageStack.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageStack.h

diff --git a/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageStack/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/.Depend
index 0cd3ef3..820894e 100644 (file)
--- a/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageStandardDeviation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageStandardDeviation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageStandardDeviation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageStandardDeviation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcImageStandardDeviation.o: mrcImageStandardDeviation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageStandardDeviation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageStandardDeviation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageStandardDeviation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageStandardDeviation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageStandardDeviation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageStandardDeviation.h

diff --git a/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/mrcImageStandardDeviation b/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/mrcImageStandardDeviation
index 783ff46..2a5d286 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/mrcImageStandardDeviation and b/src/Tools/mrcImage/mrcImageStandardDeviation/src/X86MAC64/mrcImageStandardDeviation differ

diff --git a/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/.Depend
index a5b9287..01826c9 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSubtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSubtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSubtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSubtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageSubtraction.o: mrcImageSubtraction.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageSubtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSubtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSubtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSubtraction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSubtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSubtraction.h

diff --git a/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/mrcImageSubtraction b/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/mrcImageSubtraction
index ce0aa6a..92842db 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/mrcImageSubtraction and b/src/Tools/mrcImage/mrcImageSubtraction/src/X86MAC64/mrcImageSubtraction differ

diff --git a/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/.Depend
index a380a81..de72863 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSuperResolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSuperResolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSuperResolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSuperResolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,71 +91,120 @@ mrcImageSuperResolution.o: mrcImageSuperResolution.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSuperResolution.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSuperResolution.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/nr2.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/lmrcImageSubtractionCalc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageSubtractionCalc.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSuperResolution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSuperResolution.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSuperResolution.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSuperResolution.h

diff --git a/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/mrcImageSuperResolution b/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/mrcImageSuperResolution
index 8fb9e20..78be74f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/mrcImageSuperResolution and b/src/Tools/mrcImage/mrcImageSuperResolution/src/X86MAC64/mrcImageSuperResolution differ

diff --git a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/.Depend
index c3ec9ed..50fb400 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageSymmetryAverage.o: mrcImageSymmetryAverage.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryAverage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryAverage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,15 +132,10 @@ mrcImageSymmetryAverage.o: mrcImageSymmetryAverage.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
   /Applications/Eos.app/Eos/include/lmrcImageSymmetryFind.h \
-  /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
   /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageDensity.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
@@ -105,34 +145,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryAverage.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryAverage.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryAverage.h

diff --git a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/mrcImageSymmetryAverage b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/mrcImageSymmetryAverage
index c5829e2..0fec586 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/mrcImageSymmetryAverage and b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/X86MAC64/mrcImageSymmetryAverage differ

diff --git a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/.Depend
index 6ace6df..9c4909c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryCentreFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryCentreFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryCentreFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryCentreFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,64 +92,116 @@ mrcImageSymmetryCentreFind.o: mrcImageSymmetryCentreFind.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryCentreFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryCentreFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageSymmetryFind.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryCentreFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryCentreFind.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryCentreFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryCentreFind.h

diff --git a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/mrcImageSymmetryCentreFind b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/mrcImageSymmetryCentreFind
index f4adb61..2d38772 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/mrcImageSymmetryCentreFind and b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/X86MAC64/mrcImageSymmetryCentreFind differ

diff --git a/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/.Depend
old mode 100755 (executable)
new mode 100644 (file)
index 3ff88ee..531f358
--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,31 +91,45 @@ mrcImageSymmetryFind.o: mrcImageSymmetryFind.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -95,41 +137,76 @@ mrcImageSymmetryFind.o: mrcImageSymmetryFind.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
   /Applications/Eos.app/Eos/include/lmrcImageSymmetryFind.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryFind.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageSymmetryFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageSymmetryFind.h

diff --git a/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/mrcImageSymmetryFind b/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/mrcImageSymmetryFind
index 0029004..b726de4 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/mrcImageSymmetryFind and b/src/Tools/mrcImage/mrcImageSymmetryFind/src/X86MAC64/mrcImageSymmetryFind differ

diff --git a/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/.Depend
index f1c88ef..df6dad7 100644 (file)
--- a/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTfunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTfunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTfunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTfunction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageTfunction.o: mrcImageTfunction.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTfunction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTfunction.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTfunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTfunction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTfunction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTfunction.h

diff --git a/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/mrcImageTfunction b/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/mrcImageTfunction
index 03843b2..4ccbd8c 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/mrcImageTfunction and b/src/Tools/mrcImage/mrcImageTfunction/src/X86MAC64/mrcImageTfunction differ

diff --git a/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/.Depend
index e1a5ac6..a10e3d6 100644 (file)
--- a/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,69 +91,119 @@ mrcImageTiltAxisSearch.o: mrcImageTiltAxisSearch.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/Vector.h
+  /usr/include/sys/syslimits.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearch.h

diff --git a/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/mrcImageTiltAxisSearch b/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/mrcImageTiltAxisSearch
index bb70fa5..b1491ed 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/mrcImageTiltAxisSearch and b/src/Tools/mrcImage/mrcImageTiltAxisSearch/src/X86MAC64/mrcImageTiltAxisSearch differ

diff --git a/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/.Depend
index 94b8831..e0e1c4e 100644 (file)
--- a/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearchHelp.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearchHelp.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearchHelp.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearchHelp.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,31 +92,45 @@ mrcImageTiltAxisSearchHelp.o: mrcImageTiltAxisSearchHelp.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearchHelp.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearchHelp.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -98,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearchHelp.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearchHelp.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTiltAxisSearchHelp.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTiltAxisSearchHelp.h

diff --git a/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/mrcImageTiltAxisSearchHelp b/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/mrcImageTiltAxisSearchHelp
index 6b5048e..3de30b9 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/mrcImageTiltAxisSearchHelp and b/src/Tools/mrcImage/mrcImageTiltAxisSearchHelp/src/X86MAC64/mrcImageTiltAxisSearchHelp differ

diff --git a/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/.Depend
index 38fac3c..e977c97 100644 (file)
--- a/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageToNAMDConstantForces.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageToNAMDConstantForces.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageToNAMDConstantForces.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageToNAMDConstantForces.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,64 +92,118 @@ mrcImageToNAMDConstantForces.o: mrcImageToNAMDConstantForces.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageToNAMDConstantForces.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageToNAMDConstantForces.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageToNAMDConstantForces.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageToNAMDConstantForces.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageToNAMDConstantForces.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageToNAMDConstantForces.h

diff --git a/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/mrcImageToNAMDConstantForces b/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/mrcImageToNAMDConstantForces
index d7a050a..57672bb 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/mrcImageToNAMDConstantForces and b/src/Tools/mrcImage/mrcImageToNAMDConstantForces/src/X86MAC64/mrcImageToNAMDConstantForces differ

diff --git a/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/.Depend
index 8c3273e..045a8df 100644 (file)
--- a/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageToPointsSet.o: mrcImageToPointsSet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageBinarization.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageBinarization.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageToPointsSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageToPointsSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageToPointsSet.h

diff --git a/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/mrcImageToPointsSet b/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/mrcImageToPointsSet
index f821ce1..1490226 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/mrcImageToPointsSet and b/src/Tools/mrcImage/mrcImageToPointsSet/src/X86MAC64/mrcImageToPointsSet differ

diff --git a/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/.Depend
index c0ea66c..d43db5c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTrans.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTrans.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTrans.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTrans.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcImageTrans.o: mrcImageTrans.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTrans.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTrans.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcImageMove.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageMove.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTrans.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTrans.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTrans.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTrans.h

diff --git a/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/mrcImageTrans b/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/mrcImageTrans
index 6ca4af1..5d7a2c3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/mrcImageTrans and b/src/Tools/mrcImage/mrcImageTrans/src/X86MAC64/mrcImageTrans differ

diff --git a/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/.Depend
index a38d172..5882f8b 100644 (file)
--- a/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformDescartesIntoPolar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformDescartesIntoPolar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,97 +47,161 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformDescartesIntoPolar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformDescartesIntoPolar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageTransformDescartesIntoPolar.o:  \
- mrcImageTransformDescartesIntoPolar.c /usr/include/stdio.h \
+mrcImageTransformDescartesIntoPolar.o: \
+  mrcImageTransformDescartesIntoPolar.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformDescartesIntoPolar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformDescartesIntoPolar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImageSymmetryFind.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h \
-  /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h
+  /Applications/Eos.app/Eos/include/lmrcImageTransformDescartesIntoPolar.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformDescartesIntoPolar.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformDescartesIntoPolar.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformDescartesIntoPolar.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformDescartesIntoPolar.h

diff --git a/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/mrcImageTransformDescartesIntoPolar b/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/mrcImageTransformDescartesIntoPolar
index f4cb52b..60c331a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/mrcImageTransformDescartesIntoPolar and b/src/Tools/mrcImage/mrcImageTransformDescartesIntoPolar/src/X86MAC64/mrcImageTransformDescartesIntoPolar differ

diff --git a/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/.Depend
index 7474060..3474d36 100644 (file)
--- a/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformSign.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformSign.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformSign.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformSign.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageTransformSign.o: mrcImageTransformSign.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformSign.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformSign.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformSign.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformSign.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTransformSign.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTransformSign.h

diff --git a/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/mrcImageTransformSign b/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/mrcImageTransformSign
index 352f9dd..4470c51 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/mrcImageTransformSign and b/src/Tools/mrcImage/mrcImageTransformSign/src/X86MAC64/mrcImageTransformSign differ

diff --git a/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/.Depend
index 6a7edde..4ea4a94 100644 (file)
--- a/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTranspose.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTranspose.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTranspose.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTranspose.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageTranspose.o: mrcImageTranspose.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageTranspose.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageTranspose.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTranspose.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTranspose.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageTranspose.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageTranspose.h

diff --git a/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/mrcImageTranspose b/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/mrcImageTranspose
index 694fa16..9c69f5d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/mrcImageTranspose and b/src/Tools/mrcImage/mrcImageTranspose/src/X86MAC64/mrcImageTranspose differ

diff --git a/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/.Depend
index 7a3ffbb..db5a29f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageUnbentROI.o: mrcImageUnbentROI.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageUnbentROI.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageUnbentROI.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnbentROI.h

diff --git a/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/mrcImageUnbentROI b/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/mrcImageUnbentROI
index 1b612b0..ea08a9e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/mrcImageUnbentROI and b/src/Tools/mrcImage/mrcImageUnbentROI/src/X86MAC64/mrcImageUnbentROI differ

diff --git a/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/.Depend
index 1fc3c86..501e448 100644 (file)
--- a/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageUnexpectedMassFromPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnexpectedMassFromPDB.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageUnexpectedMassFromPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnexpectedMassFromPDB.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,61 +92,114 @@ mrcImageUnexpectedMassFromPDB.o: mrcImageUnexpectedMassFromPDB.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageUnexpectedMassFromPDB.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnexpectedMassFromPDB.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/pdbFile.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageUnexpectedMassFromPDB.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnexpectedMassFromPDB.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageUnexpectedMassFromPDB.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageUnexpectedMassFromPDB.h

diff --git a/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/mrcImageUnexpectedMassFromPDB b/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/mrcImageUnexpectedMassFromPDB
index b0303c0..7eda15e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/mrcImageUnexpectedMassFromPDB and b/src/Tools/mrcImage/mrcImageUnexpectedMassFromPDB/src/X86MAC64/mrcImageUnexpectedMassFromPDB differ

diff --git a/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/.Depend
index e397462..c77d858 100644 (file)
--- a/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageUntwist.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUntwist.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageUntwist.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUntwist.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImageUntwist.o: mrcImageUntwist.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageUntwist.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageUntwist.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageUntwist.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageUntwist.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageUntwist.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageUntwist.h

diff --git a/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/mrcImageUntwist b/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/mrcImageUntwist
index 87a235d..29633e4 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/mrcImageUntwist and b/src/Tools/mrcImage/mrcImageUntwist/src/X86MAC64/mrcImageUntwist differ

diff --git a/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/.Depend
index 43e4ce1..b0e1e7f 100644 (file)
--- a/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageVarianceAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageVarianceAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,73 +92,121 @@ mrcImageVarianceAnalysis.o: mrcImageVarianceAnalysis.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageVarianceAnalysis.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceAnalysis.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImagesStatDataGet.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageVarianceAnalysis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceAnalysis.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageVarianceAnalysis.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceAnalysis.h

diff --git a/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/mrcImageVarianceAnalysis b/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/mrcImageVarianceAnalysis
index bf45adf..e3ad3a6 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/mrcImageVarianceAnalysis and b/src/Tools/mrcImage/mrcImageVarianceAnalysis/src/X86MAC64/mrcImageVarianceAnalysis differ

diff --git a/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/.Depend
index a350189..c94b838 100644 (file)
--- a/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,70 +91,120 @@ mrcImageVarianceMap.o: mrcImageVarianceMap.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcImagesStatDataGet.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageVarianceMap.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageVarianceMap.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageVarianceMap.h

diff --git a/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/mrcImageVarianceMap b/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/mrcImageVarianceMap
index 4d53803..f7e1e70 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/mrcImageVarianceMap and b/src/Tools/mrcImage/mrcImageVarianceMap/src/X86MAC64/mrcImageVarianceMap differ

diff --git a/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/.Depend
index 51e57a2..b319c5c 100644 (file)
--- a/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,70 +91,120 @@ mrcImageVolumeCalc.o: mrcImageVolumeCalc.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/nr2.h \
-  /Applications/Eos.app/Eos/include/lmrcImageVolumeCalc.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageVolumeCalc.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageVolumeCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageVolumeCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageVolumeCalc.h

diff --git a/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/mrcImageVolumeCalc b/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/mrcImageVolumeCalc
index a9b8da2..24f8cb2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/mrcImageVolumeCalc and b/src/Tools/mrcImage/mrcImageVolumeCalc/src/X86MAC64/mrcImageVolumeCalc differ

diff --git a/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/.Depend
index ebdba08..de7c8bf 100644 (file)
--- a/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageWindowing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcImageWindowing.o: mrcImageWindowing.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageWindowing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageWindowing.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -86,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageWindowing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageWindowing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageWindowing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageWindowing.h

diff --git a/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/mrcImageWindowing b/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/mrcImageWindowing
index c046934..f3000c2 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/mrcImageWindowing and b/src/Tools/mrcImage/mrcImageWindowing/src/X86MAC64/mrcImageWindowing differ

diff --git a/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/.Depend
index 48b0051..6975688 100644 (file)
--- a/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageZPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageZPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageZPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageZPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImage3DPad2.o: mrcImage3DPad2.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageZPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageZPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,22 +134,40 @@ mrcImageZPad.o: mrcImageZPad.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImageZPad.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageZPad.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -111,32 +177,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageZPad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageZPad.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcImageZPad.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageZPad.h

diff --git a/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/mrcImageZPad b/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/mrcImageZPad
index 9d36a2c..b4933c4 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/mrcImageZPad and b/src/Tools/mrcImage/mrcImageZPad/src/X86MAC64/mrcImageZPad differ

diff --git a/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/.Depend
index 669e12a..d4591e0 100644 (file)
--- a/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagepdbFileReduce.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagepdbFileReduce.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagepdbFileReduce.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagepdbFileReduce.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,64 +91,115 @@ mrcImagepdbFileReduce.o: mrcImagepdbFileReduce.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagepdbFileReduce.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagepdbFileReduce.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/pdbInfoGet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagepdbFileReduce.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagepdbFileReduce.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagepdbFileReduce.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagepdbFileReduce.h

diff --git a/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/mrcImagepdbFileReduce b/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/mrcImagepdbFileReduce
index ab27a2d..cfce809 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/mrcImagepdbFileReduce and b/src/Tools/mrcImage/mrcImagepdbFileReduce/src/X86MAC64/mrcImagepdbFileReduce differ

diff --git a/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/.Depend
index a9fca1d..84bbd9c 100644 (file)
--- a/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagesSinogramCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagesSinogramCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImagesSinogramCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagesSinogramCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,42 +92,82 @@ mrcImagesSinogramCorrelation.o: mrcImagesSinogramCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/sys/stat.h /usr/include/sys/types.h \
-  /usr/include/unistd.h /usr/include/sys/unistd.h \
-  /usr/include/sys/select.h /usr/include/sys/_select.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/sys/stat.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_nlink_t.h \
+  /usr/include/sys/_types/_gid_t.h /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_s_ifmt.h /usr/include/sys/_types/_filesec_t.h \
+  /usr/include/sys/types.h /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/unistd.h \
+  /usr/include/sys/unistd.h /usr/include/sys/_types/_posix_vdisable.h \
+  /usr/include/sys/_types/_seek_set.h /usr/include/sys/select.h \
+  /usr/include/sys/_select.h /usr/include/sys/_types/_uuid_t.h \
+  /usr/include/gethostuuid.h ../inc/config.h \
   ../inc/../inc/mrcImagesSinogramCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/lmrcImageFileListAndEulerAngleDataRead.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageSinogram.h \
   /Applications/Eos.app/Eos/include/lCommonLineCalculation.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -107,34 +175,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagesSinogramCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagesSinogramCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagesSinogramCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagesSinogramCorrelation.h

diff --git a/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/mrcImagesSinogramCorrelation b/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/mrcImagesSinogramCorrelation
index 52a9819..f5cc8ba 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/mrcImagesSinogramCorrelation and b/src/Tools/mrcImage/mrcImagesSinogramCorrelation/src/X86MAC64/mrcImagesSinogramCorrelation differ

diff --git a/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/.Depend
index f1a4b66..b2ced87 100644 (file)
--- a/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagestoRef.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagestoRef.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagestoRef.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagestoRef.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,114 @@ mrcImagestoRef.o: mrcImagestoRef.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImagestoRef.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImagestoRef.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagestoRef.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagestoRef.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImagestoRef.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImagestoRef.h

diff --git a/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/mrcImagestoRef b/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/mrcImagestoRef
index d783fce..c77408d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/mrcImagestoRef and b/src/Tools/mrcImage/mrcImagestoRef/src/X86MAC64/mrcImagestoRef differ

diff --git a/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/.Depend
index 42fc7f6..5f7e6fb 100644 (file)
--- a/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcImateToPointsSet.o: mrcImateToPointsSet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImateToPointsSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImateToPointsSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImateToPointsSet.h

diff --git a/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/mrcImateToPointsSet b/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/mrcImateToPointsSet
index a4ac408..44e07a0 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/mrcImateToPointsSet and b/src/Tools/mrcImage/mrcImateToPointsSet/src/X86MAC64/mrcImateToPointsSet differ

diff --git a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/.Depend
index 0ed133d..d651588 100644 (file)
--- a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcInfo.o: mrcInfo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,32 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcInfo.h

diff --git a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/argCheck.o b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/argCheck.o
index 370b641..6711c8d 100644 (file)
Binary files a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/argCheck.o and b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/argCheck.o differ

diff --git a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/init.o b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/init.o
index 30451a6..b99f2cb 100644 (file)
Binary files a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/init.o and b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/init.o differ

diff --git a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo
index 13956d4..30aa8e5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo and b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo differ

diff --git a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo.o b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo.o
index 6ca1ac5..650158a 100644 (file)
Binary files a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo.o and b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/mrcInfo.o differ

diff --git a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/usage.o b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/usage.o
index 77701ba..a636a87 100644 (file)
Binary files a/src/Tools/mrcImage/mrcInfo/src/X86MAC64/usage.o and b/src/Tools/mrcImage/mrcInfo/src/X86MAC64/usage.o differ

diff --git a/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/.Depend
index 3db0dbb..59107ba 100644 (file)
--- a/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcInfoSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcInfoSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcInfoSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcInfoSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcInfoSet.o: mrcInfoSet.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/mrcImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -85,32 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcInfoSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcInfoSet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcInfoSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcInfoSet.h

diff --git a/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/mrcInfoSet b/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/mrcInfoSet
index 3b554ea..4c8033b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/mrcInfoSet and b/src/Tools/mrcImage/mrcInfoSet/src/X86MAC64/mrcInfoSet differ

diff --git a/src/Tools/mrcImage/mrcMask/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcMask/src/X86MAC64/.Depend
index 1b0f867..975f6cb 100644 (file)
--- a/src/Tools/mrcImage/mrcMask/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcMask/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcMask.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMask.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcMask.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMask.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcMask.o: mrcMask.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcMask.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMask.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,32 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcMask.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcMask.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrcMask.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcMask.h

diff --git a/src/Tools/mrcImage/mrcMask/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcMask/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcMask/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcMask/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcMask/src/X86MAC64/mrcMask b/src/Tools/mrcImage/mrcMask/src/X86MAC64/mrcMask
index e0ef8a3..7bc1ade 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcMask/src/X86MAC64/mrcMask and b/src/Tools/mrcImage/mrcMask/src/X86MAC64/mrcMask differ

diff --git a/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/.Depend
index d491f6b..a26ca82 100644 (file)
--- a/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ mrcMeanYlinePos.o: mrcMeanYlinePos.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
@@ -85,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcMeanYlinePos.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcMeanYlinePos.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcMeanYlinePos.h

diff --git a/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/mrcMeanYlinePos b/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/mrcMeanYlinePos
index 95d0159..c1b1ca8 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/mrcMeanYlinePos and b/src/Tools/mrcImage/mrcMeanYlinePos/src/X86MAC64/mrcMeanYlinePos differ

diff --git a/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/.Depend
index ea082f1..f6b56d3 100644 (file)
--- a/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcMirrorImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMirrorImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcMirrorImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMirrorImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcMirrorImageCreate.o: mrcMirrorImageCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcMirrorImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcMirrorImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcMirrorImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcMirrorImageCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcMirrorImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcMirrorImageCreate.h

diff --git a/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/mrcMirrorImageCreate b/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/mrcMirrorImageCreate
index 974fbe1..eb13b75 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/mrcMirrorImageCreate and b/src/Tools/mrcImage/mrcMirrorImageCreate/src/X86MAC64/mrcMirrorImageCreate differ

diff --git a/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/.Depend
index 3f7ba10..be7bbbf 100644 (file)
--- a/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefCorEstimate.o: mrcRefCorEstimate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorEstimate.h

diff --git a/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/mrcRefCorEstimate b/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/mrcRefCorEstimate
index 8c4d34d..63cc672 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/mrcRefCorEstimate and b/src/Tools/mrcImage/mrcRefCorEstimate/src/X86MAC64/mrcRefCorEstimate differ

diff --git a/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/.Depend
index 752b4c5..78b5457 100644 (file)
--- a/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorModify.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorModify.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorModify.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorModify.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefCorModify.o: mrcRefCorModify.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorModify.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorModify.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorModify.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorModify.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorModify.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorModify.h

diff --git a/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/mrcRefCorModify b/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/mrcRefCorModify
index bdb027c..b2d4c3d 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/mrcRefCorModify and b/src/Tools/mrcImage/mrcRefCorModify/src/X86MAC64/mrcRefCorModify differ

diff --git a/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/.Depend
index 3d54995..c1e9dfa 100644 (file)
--- a/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCoreGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCoreGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCoreGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCoreGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefCoreGet.o: mrcRefCoreGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCoreGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCoreGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCoreGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCoreGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCoreGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCoreGet.h

diff --git a/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/mrcRefCoreGet b/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/mrcRefCoreGet
index 4553252..9c2c387 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/mrcRefCoreGet and b/src/Tools/mrcImage/mrcRefCoreGet/src/X86MAC64/mrcRefCoreGet differ

diff --git a/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/.Depend
index 7a7cff4..d8f4bd6 100644 (file)
--- a/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/.Depend
@@ -1,29 +1,45 @@
+AcMgADPavgc1.ltlg016.ref.pw.o: AcMgADPavgc1.ltlg016.ref.pw.c
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +48,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +92,118 @@ mrcRefCorrelation.o: mrcRefCorrelation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/mrcRefUtil.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /Applications/Eos.app/Eos/include/mrcRefUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelation.h

diff --git a/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/mrcRefCorrelation b/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/mrcRefCorrelation
index ffc7cda..dc47ee5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/mrcRefCorrelation and b/src/Tools/mrcImage/mrcRefCorrelation/src/X86MAC64/mrcRefCorrelation differ

diff --git a/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/.Depend
index 936763b..b9aa895 100644 (file)
--- a/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorrelationConv.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelationConv.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorrelationConv.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelationConv.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcRefCorrelationConv.o: mrcRefCorrelationConv.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorrelationConv.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelationConv.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorrelationConv.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelationConv.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefCorrelationConv.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefCorrelationConv.h

diff --git a/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/mrcRefCorrelationConv b/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/mrcRefCorrelationConv
index 9aefab1..8c2d972 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/mrcRefCorrelationConv and b/src/Tools/mrcImage/mrcRefCorrelationConv/src/X86MAC64/mrcRefCorrelationConv differ

diff --git a/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/.Depend
index 98a3c42..4c1da21 100644 (file)
--- a/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefEstimate.o: mrcRefEstimate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefEstimate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefEstimate.h

diff --git a/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/mrcRefEstimate b/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/mrcRefEstimate
index 9f6288f..a849145 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/mrcRefEstimate and b/src/Tools/mrcImage/mrcRefEstimate/src/X86MAC64/mrcRefEstimate differ

diff --git a/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/.Depend
index f3cea77..166e628 100644 (file)
--- a/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefFFTConvert.o: mrcRefFFTConvert.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -86,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefFFTConvert.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefFFTConvert.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefFFTConvert.h

diff --git a/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/mrcRefFFTConvert b/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/mrcRefFFTConvert
index 1f467ab..8d2cbb1 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/mrcRefFFTConvert and b/src/Tools/mrcImage/mrcRefFFTConvert/src/X86MAC64/mrcRefFFTConvert differ

diff --git a/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/.Depend
index 1c5b9db..f6e4fc1 100644 (file)
--- a/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefHeaderCreate.o: mrcRefHeaderCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefHeaderCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefHeaderCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefHeaderCreate.h

diff --git a/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/mrcRefHeaderCreate b/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/mrcRefHeaderCreate
index e021265..8659ab5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/mrcRefHeaderCreate and b/src/Tools/mrcImage/mrcRefHeaderCreate/src/X86MAC64/mrcRefHeaderCreate differ

diff --git a/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/.Depend
index ce53a6f..d5e9e7e 100644 (file)
--- a/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefHighPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefHighPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefHighPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefHighPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcRefHighPassFilter.o: mrcRefHighPassFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefHighPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefHighPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefHighPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefHighPassFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefHighPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefHighPassFilter.h

diff --git a/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/mrcRefHighPassFilter b/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/mrcRefHighPassFilter
index 166561f..bbb01d4 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/mrcRefHighPassFilter and b/src/Tools/mrcImage/mrcRefHighPassFilter/src/X86MAC64/mrcRefHighPassFilter differ

diff --git a/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/.Depend
index 7240482..9878c87 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcRefImageCorrelation.o: mrcRefImageCorrelation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageCorrelation.h

diff --git a/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/mrcRefImageCorrelation b/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/mrcRefImageCorrelation
index ffeb2bc..4c3d383 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/mrcRefImageCorrelation and b/src/Tools/mrcImage/mrcRefImageCorrelation/src/X86MAC64/mrcRefImageCorrelation differ

diff --git a/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/.Depend
index 11318c4..440982d 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageOmegaCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageOmegaCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageOmegaCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageOmegaCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcRefImageOmegaCorrelation.o: mrcRefImageOmegaCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageOmegaCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageOmegaCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageOmegaCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageOmegaCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImageOmegaCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImageOmegaCorrelation.h

diff --git a/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/mrcRefImageOmegaCorrelation b/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/mrcRefImageOmegaCorrelation
index 5426a9e..09c3847 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/mrcRefImageOmegaCorrelation and b/src/Tools/mrcImage/mrcRefImageOmegaCorrelation/src/X86MAC64/mrcRefImageOmegaCorrelation differ

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/.Depend
index 959be31..e9b859c 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcRefImagepwzCorEstimate.o: mrcRefImagepwzCorEstimate.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorEstimate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorEstimate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -92,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorEstimate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorEstimate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorEstimate.h

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/mrcRefImagepwzCorEstimate b/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/mrcRefImagepwzCorEstimate
index 8fc525e..2f57524 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/mrcRefImagepwzCorEstimate and b/src/Tools/mrcImage/mrcRefImagepwzCorEstimate/src/X86MAC64/mrcRefImagepwzCorEstimate differ

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/.Depend
index 7e379f1..e4290eb 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorModify.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorModify.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorModify.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorModify.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcRefImagepwzCorModify.o: mrcRefImagepwzCorModify.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorModify.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorModify.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorModify.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorModify.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorModify.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorModify.h

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/mrcRefImagepwzCorModify b/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/mrcRefImagepwzCorModify
index bbc4647..17c909f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/mrcRefImagepwzCorModify and b/src/Tools/mrcImage/mrcRefImagepwzCorModify/src/X86MAC64/mrcRefImagepwzCorModify differ

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/.Depend
index 7799d37..37858da 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorPeakFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorPeakFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorPeakFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorPeakFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcRefImagepwzCorPeakFind.o: mrcRefImagepwzCorPeakFind.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorPeakFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorPeakFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -92,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorPeakFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorPeakFind.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorPeakFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorPeakFind.h

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/mrcRefImagepwzCorPeakFind b/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/mrcRefImagepwzCorPeakFind
index 557c436..0c804a7 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/mrcRefImagepwzCorPeakFind and b/src/Tools/mrcImage/mrcRefImagepwzCorPeakFind/src/X86MAC64/mrcRefImagepwzCorPeakFind differ

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/.Depend
index ba8f96c..d242c65 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcRefImagepwzCorSmoothing.o: mrcRefImagepwzCorSmoothing.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorSmoothing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorSmoothing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorSmoothing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorSmoothing.h

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/mrcRefImagepwzCorSmoothing b/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/mrcRefImagepwzCorSmoothing
index c2ee1cf..0a78a5a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/mrcRefImagepwzCorSmoothing and b/src/Tools/mrcImage/mrcRefImagepwzCorSmoothing/src/X86MAC64/mrcRefImagepwzCorSmoothing differ

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/.Depend
index d89b085..a3a3faf 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcRefImagepwzCorrelation.o: mrcRefImagepwzCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelation.h

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/mrcRefImagepwzCorrelation b/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/mrcRefImagepwzCorrelation
index 8e6fd76..c050af3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/mrcRefImagepwzCorrelation and b/src/Tools/mrcImage/mrcRefImagepwzCorrelation/src/X86MAC64/mrcRefImagepwzCorrelation differ

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/.Depend
index aec239b..8c5f972 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,53 +92,107 @@ mrcRefImagepwzCorrelationByFFT.o: mrcRefImagepwzCorrelationByFFT.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagepwzCorrelationByFFT.h

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/mrcRefImagepwzCorrelationByFFT b/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/mrcRefImagepwzCorrelationByFFT
index d433956..3921e2a 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/mrcRefImagepwzCorrelationByFFT and b/src/Tools/mrcImage/mrcRefImagepwzCorrelationByFFT/src/X86MAC64/mrcRefImagepwzCorrelationByFFT differ

diff --git a/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/.Depend
index 646d7cc..6f8810a 100644 (file)
--- a/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefImagexaFit.o: mrcRefImagexaFit.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagexaFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefImagexaFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefImagexaFit.h

diff --git a/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/mrcRefImagexaFit b/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/mrcRefImagexaFit
index 0d1cd88..2d5569f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/mrcRefImagexaFit and b/src/Tools/mrcImage/mrcRefImagexaFit/src/X86MAC64/mrcRefImagexaFit differ

diff --git a/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/.Depend
index 4237ed2..3f78355 100644 (file)
--- a/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefLowPassFilter.o: mrcRefLowPassFilter.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefLowPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefLowPassFilter.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefLowPassFilter.h

diff --git a/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/mrcRefLowPassFilter b/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/mrcRefLowPassFilter
index cbfdb26..3a6daad 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/mrcRefLowPassFilter and b/src/Tools/mrcImage/mrcRefLowPassFilter/src/X86MAC64/mrcRefLowPassFilter differ

diff --git a/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/.Depend
index 5a00ac0..a6d0ad8 100644 (file)
--- a/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,118 @@ mrcRefNoiseAdd.o: mrcRefNoiseAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcRefUtil.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefNoiseAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefNoiseAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefNoiseAdd.h

diff --git a/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/mrcRefNoiseAdd b/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/mrcRefNoiseAdd
index 441e2a2..6896efc 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/mrcRefNoiseAdd and b/src/Tools/mrcImage/mrcRefNoiseAdd/src/X86MAC64/mrcRefNoiseAdd differ

diff --git a/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/.Depend
index 32b4abc..9949d1a 100644 (file)
--- a/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefNormalizing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefNormalizing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefNormalizing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefNormalizing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefNormalizing.o: mrcRefNormalizing.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefNormalizing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefNormalizing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefNormalizing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefNormalizing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefNormalizing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefNormalizing.h

diff --git a/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/mrcRefNormalizing b/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/mrcRefNormalizing
index 586df12..5e4ebf3 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/mrcRefNormalizing and b/src/Tools/mrcImage/mrcRefNormalizing/src/X86MAC64/mrcRefNormalizing differ

diff --git a/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/.Depend
index 1c39826..b3a593f 100644 (file)
--- a/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefPhaseImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefPhaseImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefPhaseImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefPhaseImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcRefPhaseImageCreate.o: mrcRefPhaseImageCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefPhaseImageCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefPhaseImageCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefPhaseImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefPhaseImageCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefPhaseImageCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefPhaseImageCreate.h

diff --git a/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/mrcRefPhaseImageCreate b/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/mrcRefPhaseImageCreate
index 6237856..0aaafbd 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/mrcRefPhaseImageCreate and b/src/Tools/mrcImage/mrcRefPhaseImageCreate/src/X86MAC64/mrcRefPhaseImageCreate differ

diff --git a/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/.Depend
index 31f27b7..84a886c 100644 (file)
--- a/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,22 +91,40 @@ mrcRefSmoothing.o: mrcRefSmoothing.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRefSmoothing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefSmoothing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -87,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefSmoothing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefSmoothing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefSmoothing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefSmoothing.h

diff --git a/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/mrcRefSmoothing b/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/mrcRefSmoothing
index 44a3600..539a36f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/mrcRefSmoothing and b/src/Tools/mrcImage/mrcRefSmoothing/src/X86MAC64/mrcRefSmoothing differ

diff --git a/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/.Depend
index 48919b4..40a4ff1 100644 (file)
--- a/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefz1ImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefz1ImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefz1ImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefz1ImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcRefz1ImageCorrelation.o: mrcRefz1ImageCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcRefz1ImageCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRefz1ImageCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefz1ImageCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefz1ImageCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRefz1ImageCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRefz1ImageCorrelation.h

diff --git a/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/mrcRefz1ImageCorrelation b/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/mrcRefz1ImageCorrelation
index 1a37eab..0b2f80b 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/mrcRefz1ImageCorrelation and b/src/Tools/mrcImage/mrcRefz1ImageCorrelation/src/X86MAC64/mrcRefz1ImageCorrelation differ

diff --git a/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/.Depend
index 6523696..9fbb144 100644 (file)
--- a/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcSinogramFET.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFET.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcSinogramFET.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFET.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ mrcSinogramFET.o: mrcSinogramFET.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcSinogramFET.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFET.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcSinogramFET.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcSinogramFET.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFET.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFET.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFET.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFET.h

diff --git a/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/mrcSinogramFET b/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/mrcSinogramFET
index ffa2805..ba4acb5 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/mrcSinogramFET and b/src/Tools/mrcImage/mrcSinogramFET/src/X86MAC64/mrcSinogramFET differ

diff --git a/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/.Depend
index e292743..71e771a 100644 (file)
--- a/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ mrcSinogramFETcalcSDforNormalize.o: mrcSinogramFETcalcSDforNormalize.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -90,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcSDforNormalize.h

diff --git a/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/mrcSinogramFETcalcSDforNormalize b/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/mrcSinogramFETcalcSDforNormalize
index 23de16e..d22fa6f 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/mrcSinogramFETcalcSDforNormalize and b/src/Tools/mrcImage/mrcSinogramFETcalcSDforNormalize/src/X86MAC64/mrcSinogramFETcalcSDforNormalize differ

diff --git a/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/.Depend
index c250a15..3a90164 100644 (file)
--- a/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcWeight.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcWeight.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcWeight.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcWeight.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,63 +92,115 @@ mrcSinogramFETcalcWeight.o: mrcSinogramFETcalcWeight.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcWeight.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcWeight.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/lmrcSinogramFETcalcWeight.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcSinogramFET.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcWeight.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcWeight.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcalcWeight.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcalcWeight.h

diff --git a/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/mrcSinogramFETcalcWeight b/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/mrcSinogramFETcalcWeight
index 036405c..7c2c66e 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/mrcSinogramFETcalcWeight and b/src/Tools/mrcImage/mrcSinogramFETcalcWeight/src/X86MAC64/mrcSinogramFETcalcWeight differ

diff --git a/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/.Depend
index 47e83b3..07ecbc6 100644 (file)
--- a/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcorrelationMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcorrelationMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcorrelationMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcorrelationMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcSinogramFETcorrelationMap.o: mrcSinogramFETcorrelationMap.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcorrelationMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcorrelationMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcSinogramFETcorrelationMap.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcSinogramFETcorrelationMap.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcorrelationMap.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcorrelationMap.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETcorrelationMap.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETcorrelationMap.h

diff --git a/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/mrcSinogramFETcorrelationMap b/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/mrcSinogramFETcorrelationMap
index dea487e..c0e5044 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/mrcSinogramFETcorrelationMap and b/src/Tools/mrcImage/mrcSinogramFETcorrelationMap/src/X86MAC64/mrcSinogramFETcorrelationMap differ

diff --git a/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/.Depend
index 679b5ec..7879d77 100644 (file)
--- a/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETnormalizedMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETnormalizedMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETnormalizedMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETnormalizedMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcSinogramFETnormalizedMap.o: mrcSinogramFETnormalizedMap.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETnormalizedMap.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETnormalizedMap.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcSinogramFETnormalizedMap.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcSinogramFETnormalizedMap.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETnormalizedMap.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETnormalizedMap.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETnormalizedMap.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETnormalizedMap.h

diff --git a/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/mrcSinogramFETnormalizedMap b/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/mrcSinogramFETnormalizedMap
index de3b63d..d935781 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/mrcSinogramFETnormalizedMap and b/src/Tools/mrcImage/mrcSinogramFETnormalizedMap/src/X86MAC64/mrcSinogramFETnormalizedMap differ

diff --git a/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/.Depend
index 198f3ea..0baed3b 100644 (file)
--- a/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETreferredCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETreferredCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETreferredCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETreferredCorrelation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,62 +92,114 @@ mrcSinogramFETreferredCorrelation.o: mrcSinogramFETreferredCorrelation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETreferredCorrelation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETreferredCorrelation.h \
   /Applications/Eos.app/Eos/include/lmrcSinogramFETreferredCorrelation.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/Array.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETreferredCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETreferredCorrelation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETreferredCorrelation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETreferredCorrelation.h

diff --git a/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/mrcSinogramFETreferredCorrelation b/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/mrcSinogramFETreferredCorrelation
index da285c2..d63e496 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/mrcSinogramFETreferredCorrelation and b/src/Tools/mrcImage/mrcSinogramFETreferredCorrelation/src/X86MAC64/mrcSinogramFETreferredCorrelation differ

diff --git a/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/.Depend
index cde2faa..9f80fae 100644 (file)
--- a/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,93 +47,159 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcSinogramFETsmoothParameterMatching.o:  \
- mrcSinogramFETsmoothParameterMatching.c /usr/include/stdio.h \
+mrcSinogramFETsmoothParameterMatching.o: \
+  mrcSinogramFETsmoothParameterMatching.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/lmrcSinogramFETsmoothParameterMatching.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcSinogramFETsmoothParameterMatching.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcSinogramFETsmoothParameterMatching.h

diff --git a/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/mrcSinogramFETsmoothParameterMatching b/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/mrcSinogramFETsmoothParameterMatching
index f4affcf..de93ffb 100755 (executable)
Binary files a/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/mrcSinogramFETsmoothParameterMatching and b/src/Tools/mrcImage/mrcSinogramFETsmoothParameterMatching/src/X86MAC64/mrcSinogramFETsmoothParameterMatching differ

diff --git a/src/Tools/mrcImage/mrcView/src/X86MAC64/.Depend b/src/Tools/mrcImage/mrcView/src/X86MAC64/.Depend
index 512db9c..a313d3d 100644 (file)
--- a/src/Tools/mrcImage/mrcView/src/X86MAC64/.Depend
+++ b/src/Tools/mrcImage/mrcView/src/X86MAC64/.Depend
@@ -1,196 +1,69 @@
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-  /usr/include/sys/_types.h /usr/include/sys/cdefs.h \
-  /usr/include/machine/_types.h /usr/include/i386/_types.h \
-  /usr/include/stdlib.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/sys/wait.h \
-  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
-  /usr/include/machine/signal.h /usr/include/i386/signal.h \
-  /usr/include/i386/_structs.h /usr/include/sys/_structs.h \
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-  /usr/include/sys/resource.h /usr/include/machine/endian.h \
-  /usr/include/i386/endian.h /usr/include/sys/_endian.h \
-  /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /usr/include/tk.h /usr/include/tcl.h \
-  /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stdarg.h \
-  /usr/include/tclDecls.h /usr/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stddef.h \
-  /usr/include/tkDecls.h
-eosmrcView.o: eosmrcView.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
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-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
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-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h
-eosmrcView.o: eosmrcView.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
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-  /usr/include/i386/_types.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
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-eosmrcView.o: eosmrcView.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
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-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
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 eosmrcView.o: eosmrcView.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
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-eosmrcView.o: eosmrcView.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
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-  /usr/include/i386/_types.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h
-eosmrcView.o: eosmrcView.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
-  /usr/include/machine/endian.h /usr/include/i386/endian.h \
-  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
-  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
-  /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
-  /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h
-eosmrcView.o: eosmrcView.cc /usr/include/stdio.h /usr/include/sys/cdefs.h \
-  /usr/include/sys/_symbol_aliasing.h \
-  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
-  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
-  /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tk.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tcl.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stdarg.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdarg.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclDecls.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tclPlatDecls.h \
-  /usr/include/X11/Xlib.h /usr/include/sys/types.h /usr/include/X11/X.h \
+  /usr/include/X11/Xlib.h /usr/include/sys/types.h \
+  /usr/include/sys/_types/_blkcnt_t.h \
+  /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \
+  /usr/include/sys/_types/_in_addr_t.h \
+  /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \
+  /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \
+  /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_useconds_t.h \
+  /usr/include/sys/_types/_suseconds_t.h \
+  /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \
+  /usr/include/sys/_types/_fd_def.h \
+  /usr/include/sys/_types/_fd_setsize.h \
+  /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \
+  /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \
+  /usr/include/sys/_types/_fd_copy.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_fsblkcnt_t.h \
+  /usr/include/sys/_types/_fsfilcnt_t.h /usr/include/X11/X.h \
   /usr/include/X11/Xfuncproto.h /usr/include/X11/Xosdefs.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/stddef.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stddef.h \
   /Applications/Eos.app/Eos/util/X86MAC64/include/tkDecls.h

diff --git a/src/Tools/mrcImage/mrcView/src/X86MAC64/Makefile b/src/Tools/mrcImage/mrcView/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/mrcImage/mrcView/src/X86MAC64/Makefile
+++ b/src/Tools/mrcImage/mrcView/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/gmolvie/src/X86MAC64/.Depend b/src/Tools/openGL/gmolvie/src/X86MAC64/.Depend
index 70e5c9c..f65597d 100644 (file)
--- a/src/Tools/openGL/gmolvie/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/gmolvie/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/gmolvie.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/gmolvie.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,19 +47,38 @@ gmolvie.o: gmolvie.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/gmolvie.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/gmolvie.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/openGL.h
 init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/gmolvie.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/gmolvie.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,32 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/gmolvie.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/gmolvie.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/gmolvie.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/gmolvie.h

diff --git a/src/Tools/openGL/gmolvie/src/X86MAC64/Makefile b/src/Tools/openGL/gmolvie/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/gmolvie/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/gmolvie/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/gmolvie/src/X86MAC64/gmolvie b/src/Tools/openGL/gmolvie/src/X86MAC64/gmolvie
index a4ac408..44e07a0 100755 (executable)
Binary files a/src/Tools/openGL/gmolvie/src/X86MAC64/gmolvie and b/src/Tools/openGL/gmolvie/src/X86MAC64/gmolvie differ

diff --git a/src/Tools/openGL/molvie/src/X86MAC64/.Depend b/src/Tools/openGL/molvie/src/X86MAC64/.Depend
index d2aa1c7..4b84fc0 100644 (file)
--- a/src/Tools/openGL/molvie/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/molvie/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvie.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvie.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,61 +47,168 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvie.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvie.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
+molvie.o: molvie.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/util/X86MAC64/include/GL/glut.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/OpenGLAvailability.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gl.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gltypes.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glext.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glu.h \
+  ../inc/config.h ../inc/../inc/molvie.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/openGL.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Array.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/molvieDefault.h \
+  /Applications/Eos.app/Eos/include/lmolvie.h \
+  /Applications/Eos.app/Eos/include/Contour.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvie.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvie.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvie.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvie.h

diff --git a/src/Tools/openGL/molvie/src/X86MAC64/Makefile b/src/Tools/openGL/molvie/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/molvie/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/molvie/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/molvieDock/src/X86MAC64/.Depend b/src/Tools/openGL/molvieDock/src/X86MAC64/.Depend
index 0093365..431ddf2 100644 (file)
--- a/src/Tools/openGL/molvieDock/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/molvieDock/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieDock.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieDock.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,61 +47,168 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieDock.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieDock.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
+molvieDock.o: molvieDock.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/util/X86MAC64/include/GL/glut.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/OpenGLAvailability.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gl.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gltypes.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glext.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glu.h \
+  ../inc/config.h ../inc/../inc/molvieDock.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/openGL.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Array.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/molvieDockDefault.h \
+  /Applications/Eos.app/Eos/include/lmolvie.h \
+  /Applications/Eos.app/Eos/include/Contour.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvieDock.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieDock.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvieDock.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieDock.h

diff --git a/src/Tools/openGL/molvieDock/src/X86MAC64/Makefile b/src/Tools/openGL/molvieDock/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/molvieDock/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/molvieDock/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/molvieFlight/src/X86MAC64/.Depend b/src/Tools/openGL/molvieFlight/src/X86MAC64/.Depend
index b7e5481..0715e82 100644 (file)
--- a/src/Tools/openGL/molvieFlight/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/molvieFlight/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieFlight.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieFlight.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,61 +47,168 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieFlight.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieFlight.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
+molvieFlight.o: molvieFlight.c /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/util/X86MAC64/include/GL/glut.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/OpenGLAvailability.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gl.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gltypes.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glext.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glu.h \
+  ../inc/config.h ../inc/../inc/molvieFlight.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/openGL.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Array.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/molvieFlightDefault.h \
+  /Applications/Eos.app/Eos/include/lmolvie.h \
+  /Applications/Eos.app/Eos/include/Contour.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvieFlight.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieFlight.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvieFlight.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieFlight.h

diff --git a/src/Tools/openGL/molvieFlight/src/X86MAC64/Makefile b/src/Tools/openGL/molvieFlight/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/molvieFlight/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/molvieFlight/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/.Depend b/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/.Depend
index 67d03f7..b9942bc 100644 (file)
--- a/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieMrcViewer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieMrcViewer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,63 +47,168 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieMrcViewer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieMrcViewer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
+molvieMrcViewer.o: molvieMrcViewer.c /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/util/X86MAC64/include/GL/glut.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/OpenGLAvailability.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gl.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gltypes.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glext.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glu.h \
+  ../inc/config.h ../inc/../inc/molvieMrcViewer.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/openGL.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Array.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/molvieMrcViewerDefault.h \
+  /Applications/Eos.app/Eos/include/lmolvie.h \
+  /Applications/Eos.app/Eos/include/Contour.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/molvieMrcViewer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieMrcViewer.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/molvieMrcViewer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieMrcViewer.h

diff --git a/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/Makefile b/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/molvieMrcViewer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/molvieProjection/src/X86MAC64/.Depend b/src/Tools/openGL/molvieProjection/src/X86MAC64/.Depend
index 1578004..76e5cc2 100644 (file)
--- a/src/Tools/openGL/molvieProjection/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/molvieProjection/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,63 +47,168 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieProjection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieProjection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
+molvieProjection.o: molvieProjection.c /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/util/X86MAC64/include/GL/glut.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/OpenGLAvailability.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gl.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gltypes.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glext.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glu.h \
+  ../inc/config.h ../inc/../inc/molvieProjection.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/openGL.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Array.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/molvieProjectionDefault.h \
+  /Applications/Eos.app/Eos/include/lmolvie.h \
+  /Applications/Eos.app/Eos/include/Contour.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/molvieProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieProjection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/molvieProjection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieProjection.h

diff --git a/src/Tools/openGL/molvieProjection/src/X86MAC64/Makefile b/src/Tools/openGL/molvieProjection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/molvieProjection/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/molvieProjection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/molvieViewer/src/X86MAC64/.Depend b/src/Tools/openGL/molvieViewer/src/X86MAC64/.Depend
index 328d688..3849d82 100644 (file)
--- a/src/Tools/openGL/molvieViewer/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/molvieViewer/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieViewer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieViewer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,61 +47,168 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/molvieViewer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/molvieViewer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
+molvieViewer.o: molvieViewer.c /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+  /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
+  /usr/include/AvailabilityInternal.h /usr/include/_types.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
+  /usr/include/machine/endian.h /usr/include/i386/endian.h \
+  /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+  /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/util/X86MAC64/include/GL/glut.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/OpenGLAvailability.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gl.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/gltypes.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glext.h \
+  /System/Library/Frameworks/OpenGL.framework/Headers/glu.h \
+  ../inc/config.h ../inc/../inc/molvieViewer.h \
+  /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/openGL.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
+  /Applications/Eos.app/Eos/include/Matrix3D.h \
+  /Applications/Eos.app/Eos/include/Vector.h \
+  /Applications/Eos.app/Eos/include/Array.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h \
+  /Applications/Eos.app/Eos/include/molvieViewerDefault.h \
+  /Applications/Eos.app/Eos/include/lmolvie.h \
+  /Applications/Eos.app/Eos/include/Contour.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvieViewer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieViewer.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/molvieViewer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/molvieViewer.h

diff --git a/src/Tools/openGL/molvieViewer/src/X86MAC64/Makefile b/src/Tools/openGL/molvieViewer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/molvieViewer/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/molvieViewer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/rasmonyo/src/X86MAC64/.Depend b/src/Tools/openGL/rasmonyo/src/X86MAC64/.Depend
index 119d3cd..4a02fb9 100644 (file)
--- a/src/Tools/openGL/rasmonyo/src/X86MAC64/.Depend
+++ b/src/Tools/openGL/rasmonyo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/rasmonyo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/rasmonyo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/rasmonyo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/rasmonyo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ rasmonyo.o: rasmonyo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/rasmonyo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/rasmonyo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/openGL.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -81,32 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/rasmonyo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/rasmonyo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/rasmonyo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/rasmonyo.h

diff --git a/src/Tools/openGL/rasmonyo/src/X86MAC64/Makefile b/src/Tools/openGL/rasmonyo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/openGL/rasmonyo/src/X86MAC64/Makefile
+++ b/src/Tools/openGL/rasmonyo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/openGL/rasmonyo/src/X86MAC64/rasmonyo b/src/Tools/openGL/rasmonyo/src/X86MAC64/rasmonyo
index a4ac408..44e07a0 100755 (executable)
Binary files a/src/Tools/openGL/rasmonyo/src/X86MAC64/rasmonyo and b/src/Tools/openGL/rasmonyo/src/X86MAC64/rasmonyo differ

diff --git a/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/.Depend
index 6b95ca2..3284be3 100644 (file)
--- a/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2SketchMacro.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2SketchMacro.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2SketchMacro.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2SketchMacro.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,114 @@ pdb2SketchMacro.o: pdb2SketchMacro.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2SketchMacro.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2SketchMacro.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdb2SketchMacro.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2SketchMacro.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdb2SketchMacro.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2SketchMacro.h

diff --git a/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/pdb2SketchMacro b/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/pdb2SketchMacro
index 6d62290..1223abb 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/pdb2SketchMacro and b/src/Tools/pdbUtil/pdb2SketchMacro/src/X86MAC64/pdb2SketchMacro differ

diff --git a/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/.Depend
index aeef5f6..ed05cea 100644 (file)
--- a/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2bender.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2bender.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2bender.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2bender.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,51 +91,108 @@ pdb2bender.o: pdb2bender.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2bender.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2bender.h \
   /Applications/Eos.app/Eos/include/genUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2bender.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2bender.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2bender.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2bender.h

diff --git a/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/pdb2bender b/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/pdb2bender
index 5426a9e..09c3847 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/pdb2bender and b/src/Tools/pdbUtil/pdb2bender/src/X86MAC64/pdb2bender differ

diff --git a/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/.Depend
index 80cd566..e81976d 100644 (file)
--- a/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,116 @@ pdb2mrc.o: pdb2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lpdb2mrcInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/pdbInfoGet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc.h

diff --git a/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/pdb2mrc b/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/pdb2mrc
index cca8834..da66e49 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/pdb2mrc and b/src/Tools/pdbUtil/pdb2mrc/src/X86MAC64/pdb2mrc differ

diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/.Depend
index 280e1f4..6bce81b 100644 (file)
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc2d.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2d.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc2d.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2d.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,115 @@ pdb2mrc2d.o: pdb2mrc2d.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/mrcImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h ../inc/config.h \
   ../inc/../inc/pdb2mrc2d.h /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lpdb2mrcInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Map2D.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2mrc2d.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2d.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdb2mrc2d.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2d.h

diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/pdb2mrc2d b/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/pdb2mrc2d
index a646e40..937ba2c 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/pdb2mrc2d and b/src/Tools/pdbUtil/pdb2mrc2d/src/X86MAC64/pdb2mrc2d differ

diff --git a/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/.Depend
index 9bb9f4b..03282bf 100644 (file)
--- a/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,71 +91,120 @@ pdb2mrc2dWithCTF.o: pdb2mrc2dWithCTF.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lpdb2mrcInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdb2mrc2dWithCTF.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdb2mrc2dWithCTF.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdb2mrc2dWithCTF.h

diff --git a/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/.Depend
index b7f06e4..39218bc 100644 (file)
--- a/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbAtomSection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbAtomSection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbAtomSection.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbAtomSection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,71 +91,121 @@ pdbAtomSection.o: pdbAtomSection.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/mrcImage.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/psFile.h \
-  /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/Vector.h ../inc/config.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/psFile.h \
+  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
   ../inc/../inc/pdbAtomSection.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbAtomSection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbAtomSection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbAtomSection.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbAtomSection.h

diff --git a/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/pdbAtomSection b/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/pdbAtomSection
index 79b13e6..ff8250f 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/pdbAtomSection and b/src/Tools/pdbUtil/pdbAtomSection/src/X86MAC64/pdbAtomSection differ

diff --git a/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/.Depend
old mode 100755 (executable)
new mode 100644 (file)
index 685e299..ebdb647
--- a/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCAOnly.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCAOnly.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCAOnly.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCAOnly.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ pdbCAOnly.o: pdbCAOnly.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCAOnly.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCAOnly.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -86,32 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbCAOnly.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbCAOnly.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbCAOnly.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbCAOnly.h

diff --git a/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/pdbCAOnly b/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/pdbCAOnly
index 182741d..d872ac4 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/pdbCAOnly and b/src/Tools/pdbUtil/pdbCAOnly/src/X86MAC64/pdbCAOnly differ

diff --git a/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/.Depend
index da1a79a..23cfbe8 100644 (file)
--- a/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbChargeFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbChargeFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbChargeFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbChargeFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,58 +91,114 @@ pdbChargeFit.o: pdbChargeFit.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/pdbFile.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h ../inc/config.h \
+  /Applications/Eos.app/Eos/include/ctfInfo.h ../inc/config.h \
   ../inc/../inc/pdbChargeFit.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbChargeFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbChargeFit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbChargeFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbChargeFit.h

diff --git a/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/pdbChargeFit b/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/pdbChargeFit
index 6a10841..fb58611 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/pdbChargeFit and b/src/Tools/pdbUtil/pdbChargeFit/src/X86MAC64/pdbChargeFit differ

diff --git a/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/.Depend
index 395a01e..c04445b 100644 (file)
--- a/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCoordAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCoordAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCoordAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCoordAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,115 @@ pdbCoordAdd.o: pdbCoordAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCoordAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCoordAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lpdbCoord.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/lpdbCoord.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbCoordAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbCoordAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbCoordAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbCoordAdd.h

diff --git a/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/pdbCoordAdd b/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/pdbCoordAdd
index d265f41..5365657 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/pdbCoordAdd and b/src/Tools/pdbUtil/pdbCoordAdd/src/X86MAC64/pdbCoordAdd differ

diff --git a/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/.Depend
index af57d32..c2812af 100644 (file)
--- a/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCrystalCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCrystalCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCrystalCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCrystalCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,115 @@ pdbCrystalCreate.o: pdbCrystalCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbCrystalCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbCrystalCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Crystal.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbCrystalCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbCrystalCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbCrystalCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbCrystalCreate.h

diff --git a/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/pdbCrystalCreate b/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/pdbCrystalCreate
index a530949..67364a7 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/pdbCrystalCreate and b/src/Tools/pdbUtil/pdbCrystalCreate/src/X86MAC64/pdbCrystalCreate differ

diff --git a/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/.Depend
index 4bacb87..dcfcce7 100644 (file)
--- a/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbDisplay.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbDisplay.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbDisplay.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbDisplay.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,50 +91,107 @@ pdbDisplay.o: pdbDisplay.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbDisplay.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbDisplay.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbDisplay.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbDisplay.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbDisplay.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbDisplay.h

diff --git a/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/pdbDisplay b/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/pdbDisplay
index d433956..3921e2a 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/pdbDisplay and b/src/Tools/pdbUtil/pdbDisplay/src/X86MAC64/pdbDisplay differ

diff --git a/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/.Depend
index e2888f5..f30e4e9 100644 (file)
--- a/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbFileMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbFileMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbFileMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbFileMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,58 +91,114 @@ pdbFileMerge.o: pdbFileMerge.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbFileMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbFileMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbFileMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbFileMerge.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbFileMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbFileMerge.h

diff --git a/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/pdbFileMerge b/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/pdbFileMerge
index 27d10ac..a3b49d6 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/pdbFileMerge and b/src/Tools/pdbUtil/pdbFileMerge/src/X86MAC64/pdbFileMerge differ

diff --git a/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/.Depend
index 81649ec..7a1e33d 100644 (file)
--- a/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbHelix.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbHelix.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbHelix.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbHelix.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,64 +91,119 @@ pdbHelix.o: pdbHelix.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/time.h /usr/include/_structs.h /usr/include/math.h \
-  ../inc/config.h ../inc/../inc/pdbHelix.h \
-  /Applications/Eos.app/Eos/include/Random.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/time.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h /usr/include/math.h ../inc/config.h \
+  ../inc/../inc/pdbHelix.h /Applications/Eos.app/Eos/include/Random.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lpdb2mrcInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/pdbInfoGet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbHelix.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbHelix.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbHelix.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbHelix.h

diff --git a/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/pdbHelix b/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/pdbHelix
index 5b5ca5f..cb81221 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/pdbHelix and b/src/Tools/pdbUtil/pdbHelix/src/X86MAC64/pdbHelix differ

diff --git a/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/.Depend
index 41fdd20..efd1102 100644 (file)
--- a/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbHomologySearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbHomologySearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbHomologySearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbHomologySearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ pdbHomologySearch.o: pdbHomologySearch.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbHomologySearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbHomologySearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/pdbFile.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbHomologySearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbHomologySearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbHomologySearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbHomologySearch.h

diff --git a/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbHomologySearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/.Depend
index 01e2c4d..ba983b0 100644 (file)
--- a/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,115 @@ pdbInfo.o: pdbInfo.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbInfo.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/pdbInfoGet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbInfo.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbInfo.h

diff --git a/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/pdbInfo b/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/pdbInfo
index 3e3d1f2..42a6191 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/pdbInfo and b/src/Tools/pdbUtil/pdbInfo/src/X86MAC64/pdbInfo differ

diff --git a/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/.Depend
index 6e0edbb..b34362d 100644 (file)
--- a/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,25 +91,41 @@ pdbListRMSDCalc.o: pdbListRMSDCalc.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
@@ -88,67 +134,120 @@ pdbListRMSDCalc.o: pdbListRMSDCalc.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 pdbListRMSDCalc0404.o: pdbListRMSDCalc0404.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbListRMSDCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbListRMSDCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbListRMSDCalc.h

diff --git a/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/pdbListRMSDCalc b/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/pdbListRMSDCalc
index b831b1f..8ff2a92 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/pdbListRMSDCalc and b/src/Tools/pdbUtil/pdbListRMSDCalc/src/X86MAC64/pdbListRMSDCalc differ

diff --git a/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/.Depend
index 9046173..e91a219 100644 (file)
--- a/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbListVectorCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbListVectorCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbListVectorCalc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbListVectorCalc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbListVectorCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbListVectorCalc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbListVectorCalc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbListVectorCalc.h

diff --git a/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbListVectorCalc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/.Depend
index faaf56e..e35a99b 100644 (file)
--- a/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbMatrixCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMatrixCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbMatrixCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMatrixCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ pdbMatrixCreate.o: pdbMatrixCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbMatrixCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMatrixCreate.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -81,41 +130,76 @@ pdbMatrixCreate.o: pdbMatrixCreate.c /usr/include/stdio.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/nr2.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbMatrixCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbMatrixCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbMatrixCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbMatrixCreate.h

diff --git a/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbMatrixCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/.Depend
index c16498a..281c208 100644 (file)
--- a/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbMolecularInterfaceFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMolecularInterfaceFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbMolecularInterfaceFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMolecularInterfaceFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,27 +92,44 @@ pdbMolecularInterfaceFind.o: pdbMolecularInterfaceFind.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbMolecularInterfaceFind.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMolecularInterfaceFind.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/nr2.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -92,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbMolecularInterfaceFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbMolecularInterfaceFind.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbMolecularInterfaceFind.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbMolecularInterfaceFind.h

diff --git a/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/pdbMolecularInterfaceFind b/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/pdbMolecularInterfaceFind
index f67894f..7b608bd 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/pdbMolecularInterfaceFind and b/src/Tools/pdbUtil/pdbMolecularInterfaceFind/src/X86MAC64/pdbMolecularInterfaceFind differ

diff --git a/src/Tools/pdbUtil/pdbMove/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbMove/src/X86MAC64/.Depend
index 676b056..4c1e28a 100644 (file)
--- a/src/Tools/pdbUtil/pdbMove/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbMove/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbMove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbMove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,115 @@ pdbMove.o: pdbMove.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbMove.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbMove.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
+  /Applications/Eos.app/Eos/include/pdbInfoGet.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbMove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbMove.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbMove.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbMove.h

diff --git a/src/Tools/pdbUtil/pdbMove/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbMove/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbMove/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbMove/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbMove/src/X86MAC64/pdbMove b/src/Tools/pdbUtil/pdbMove/src/X86MAC64/pdbMove
index 25252af..d51a795 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbMove/src/X86MAC64/pdbMove and b/src/Tools/pdbUtil/pdbMove/src/X86MAC64/pdbMove differ

diff --git a/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/.Depend
index 6f12a09..d3ee387 100644 (file)
--- a/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbNAMDRestraintCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbNAMDRestraintCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbNAMDRestraintCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbNAMDRestraintCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,61 +91,114 @@ pdbNAMDRestraintCreate.o: pdbNAMDRestraintCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbNAMDRestraintCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbNAMDRestraintCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbNAMDRestraintCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbNAMDRestraintCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbNAMDRestraintCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbNAMDRestraintCreate.h

diff --git a/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/pdbNAMDRestraintCreate b/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/pdbNAMDRestraintCreate
index 41c93dc..0c82bf0 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/pdbNAMDRestraintCreate and b/src/Tools/pdbUtil/pdbNAMDRestraintCreate/src/X86MAC64/pdbNAMDRestraintCreate differ

diff --git a/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/.Depend
index e62a616..f798759 100644 (file)
--- a/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,62 +91,115 @@ pdbNearAtomListShow.o: pdbNearAtomListShow.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lpdbCoordInfo.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/lpdbCoordInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbNearAtomListShow.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbNearAtomListShow.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbNearAtomListShow.h

diff --git a/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/pdbNearAtomListShow b/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/pdbNearAtomListShow
index 8f24b93..813aec4 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/pdbNearAtomListShow and b/src/Tools/pdbUtil/pdbNearAtomListShow/src/X86MAC64/pdbNearAtomListShow differ

diff --git a/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/.Depend
index eb49cbb..8862a0b 100644 (file)
--- a/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbOneProteinGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbOneProteinGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbOneProteinGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbOneProteinGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,114 @@ pdbOneProteinGet.o: pdbOneProteinGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbOneProteinGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbOneProteinGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbOneProteinGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbOneProteinGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbOneProteinGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbOneProteinGet.h

diff --git a/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/pdbOneProteinGet b/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/pdbOneProteinGet
index 52c35b6..bcbc2d0 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/pdbOneProteinGet and b/src/Tools/pdbUtil/pdbOneProteinGet/src/X86MAC64/pdbOneProteinGet differ

diff --git a/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/.Depend
index 5cb30f5..d00c543 100644 (file)
--- a/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbPCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbPCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbPCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbPCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,60 +91,114 @@ pdbPCA.o: pdbPCA.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbPCA.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbPCA.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbPCA.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbPCA.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbPCA.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbPCA.h

diff --git a/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/pdbPCA b/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/pdbPCA
index 26a8237..2585039 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/pdbPCA and b/src/Tools/pdbUtil/pdbPCA/src/X86MAC64/pdbPCA differ

diff --git a/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/.Depend
index 2058706..ff45e7f 100644 (file)
--- a/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbProteinIDSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbProteinIDSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbProteinIDSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbProteinIDSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,19 +91,38 @@ pdbProteinIDSet.o: pdbProteinIDSet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbProteinIDSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbProteinIDSet.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -86,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbProteinIDSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbProteinIDSet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbProteinIDSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbProteinIDSet.h

diff --git a/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/pdbProteinIDSet b/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/pdbProteinIDSet
index 6e60265..50d484a 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/pdbProteinIDSet and b/src/Tools/pdbUtil/pdbProteinIDSet/src/X86MAC64/pdbProteinIDSet differ

diff --git a/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/.Depend
index 9529eeb..1b62918 100644 (file)
--- a/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRhoFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRhoFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,66 +91,118 @@ pdbRhoFit.o: pdbRhoFit.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h ../inc/config.h ../inc/../inc/pdbRhoFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/pdbFile.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbRhoFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbRhoFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFit.h

diff --git a/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/pdbRhoFit b/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/pdbRhoFit
index 438d2f8..2dc7173 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/pdbRhoFit and b/src/Tools/pdbUtil/pdbRhoFit/src/X86MAC64/pdbRhoFit differ

diff --git a/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/.Depend
index 86580ac..0be30b3 100644 (file)
--- a/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRhoFitCoiledCoil.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitCoiledCoil.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRhoFitCoiledCoil.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitCoiledCoil.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbRhoFitCoiledCoil.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitCoiledCoil.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbRhoFitCoiledCoil.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitCoiledCoil.h

diff --git a/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbRhoFitCoiledCoil/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/.Depend
index e8d8544..0aa74cd 100644 (file)
--- a/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRhoFitTm.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitTm.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRhoFitTm.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitTm.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,66 +91,119 @@ pdbRhoFitTm.o: pdbRhoFitTm.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h ../inc/config.h \
-  ../inc/../inc/pdbRhoFitTm.h /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
+  ../inc/../inc/pdbRhoFitTm.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/pdbFile.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbRhoFitTm.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitTm.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbRhoFitTm.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRhoFitTm.h

diff --git a/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/pdbRhoFitTm b/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/pdbRhoFitTm
index 8658143..c490889 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/pdbRhoFitTm and b/src/Tools/pdbUtil/pdbRhoFitTm/src/X86MAC64/pdbRhoFitTm differ

diff --git a/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/.Depend
index ca519e9..c54d9be 100644 (file)
--- a/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRotation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,58 +91,114 @@ pdbRotation.o: pdbRotation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbRotation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbRotation.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
+  /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRotation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbRotation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbRotation.h

diff --git a/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/pdbRotation b/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/pdbRotation
index 4c2e058..9f34ae5 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/pdbRotation and b/src/Tools/pdbUtil/pdbRotation/src/X86MAC64/pdbRotation differ

diff --git a/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/.Depend
index 51433c6..da9a2ea 100644 (file)
--- a/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbSecondaryStructurePrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbSecondaryStructurePrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbSecondaryStructurePrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbSecondaryStructurePrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,61 +92,114 @@ pdbSecondaryStructurePrint.o: pdbSecondaryStructurePrint.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pdbSecondaryStructurePrint.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbSecondaryStructurePrint.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbSecondaryStructurePrint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbSecondaryStructurePrint.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbSecondaryStructurePrint.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbSecondaryStructurePrint.h

diff --git a/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/pdbSecondaryStructurePrint b/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/pdbSecondaryStructurePrint
index 58ad266..12cfbd8 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/pdbSecondaryStructurePrint and b/src/Tools/pdbUtil/pdbSecondaryStructurePrint/src/X86MAC64/pdbSecondaryStructurePrint differ

diff --git a/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/.Depend
index b023cf3..6b4c2e2 100644 (file)
--- a/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbShapeFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbShapeFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbShapeFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbShapeFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,63 +91,117 @@ pdbShapeFit.o: pdbShapeFit.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbShapeFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbShapeFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageContourSurface.h \
   /Applications/Eos.app/Eos/include/lpdbSurface.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/lpdb2mrcInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbShapeFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbShapeFit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbShapeFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbShapeFit.h

diff --git a/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/pdbShapeFit b/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/pdbShapeFit
index 553d48d..257f547 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/pdbShapeFit and b/src/Tools/pdbUtil/pdbShapeFit/src/X86MAC64/pdbShapeFit differ

diff --git a/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/.Depend
index ed5922c..bc7c4cd 100644 (file)
--- a/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbSurface.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbSurface.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbSurface.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbSurface.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,116 @@ pdbSurface.o: pdbSurface.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbSurface.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbSurface.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lpdbSurface.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/lpdb2mrcInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbSurface.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbSurface.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbSurface.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbSurface.h

diff --git a/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/pdbSurface b/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/pdbSurface
index eb2bdce..0685348 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/pdbSurface and b/src/Tools/pdbUtil/pdbSurface/src/X86MAC64/pdbSurface differ

diff --git a/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/.Depend
index e7811dc..da7b38a 100644 (file)
--- a/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTempFactorSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTempFactorSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTempFactorSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTempFactorSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,61 +91,114 @@ pdbTempFactorSet.o: pdbTempFactorSet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTempFactorSet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTempFactorSet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbTempFactorSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbTempFactorSet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbTempFactorSet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbTempFactorSet.h

diff --git a/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/pdbTempFactorSet b/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/pdbTempFactorSet
index 8db83a5..29f0707 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/pdbTempFactorSet and b/src/Tools/pdbUtil/pdbTempFactorSet/src/X86MAC64/pdbTempFactorSet differ

diff --git a/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/.Depend
index 915005f..0fffca7 100644 (file)
--- a/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTrans.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTrans.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTrans.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTrans.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,114 @@ pdbTrans.o: pdbTrans.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTrans.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTrans.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/genUtil.h
+  /Applications/Eos.app/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbTrans.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbTrans.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbTrans.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbTrans.h

diff --git a/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/pdbTrans b/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/pdbTrans
index cadb9c3..4b2ded9 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/pdbTrans and b/src/Tools/pdbUtil/pdbTrans/src/X86MAC64/pdbTrans differ

diff --git a/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/.Depend
index b1ca48f..ec2f4b2 100644 (file)
--- a/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,63 +91,115 @@ pdbTwoProteinFit.o: pdbTwoProteinFit.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/lpdbSelectedAtom.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h
+  /Applications/Eos.app/Eos/include/lpdbSelectedAtom.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbTwoProteinFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pdbTwoProteinFit.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbTwoProteinFit.h

diff --git a/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/pdbTwoProteinFit b/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/pdbTwoProteinFit
index 4c3b937..745395f 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/pdbTwoProteinFit and b/src/Tools/pdbUtil/pdbTwoProteinFit/src/X86MAC64/pdbTwoProteinFit differ

diff --git a/src/Tools/pdbUtil/pdbView/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbView/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbView/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbView/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/.Depend b/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/.Depend
index 79b7cfe..11c9e40 100644 (file)
--- a/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbWaterAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbWaterAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbWaterAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbWaterAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,81 +91,159 @@ pdbWaterAdd.o: pdbWaterAdd.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/pdbWaterAdd.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pdbWaterAdd.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/pdbFile.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/pdbInfoGet.h \
-  /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/lpdb2mrcInfo.h
 randwater27.o: randwater27.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/math.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/time.h /usr/include/_structs.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/time.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbWaterAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbWaterAdd.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/pdbWaterAdd.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pdbWaterAdd.h

diff --git a/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/Makefile b/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/pdbWaterAdd b/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/pdbWaterAdd
index 20b256a..30ec93e 100755 (executable)
Binary files a/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/pdbWaterAdd and b/src/Tools/pdbUtil/pdbWaterAdd/src/X86MAC64/pdbWaterAdd differ

diff --git a/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/.Depend b/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/.Depend
index 84c69ed..3c88dde 100644 (file)
--- a/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/.Depend
+++ b/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/vector2pdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/vector2pdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/vector2pdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/vector2pdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,115 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/vector2pdb.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/vector2pdb.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/vector2pdb.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/vector2pdb.h
 vector2pdb.o: vector2pdb.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/vector2pdb.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/vector2pdb.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/pdbFile.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h

diff --git a/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/Makefile b/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/Makefile
+++ b/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/vector2pdb b/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/vector2pdb
index e38e7c1..0b38e8d 100755 (executable)
Binary files a/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/vector2pdb and b/src/Tools/pdbUtil/vector2pdb/src/X86MAC64/vector2pdb differ

diff --git a/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/.Depend b/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/.Depend
index 0428b17..45570cd 100644 (file)
--- a/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/.Depend
+++ b/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleExtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleExtraction.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleExtraction.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleExtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleExtraction.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleExtraction.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleExtraction.h

diff --git a/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/Makefile b/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/Makefile
+++ b/src/Tools/pickup/mrcImageNeuralNetParticleExtraction/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/.Depend b/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/.Depend
index 138e73c..f8da8e7 100644 (file)
--- a/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/.Depend
+++ b/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleLearning.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleLearning.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleLearning.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleLearning.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,106 +92,174 @@ mrcImageNeuralNetParticleLearning.o: mrcImageNeuralNetParticleLearning.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
   ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleLearning.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/NeuralNet.h \
-  /Applications/Eos.app/Eos/include/lmrcNeuralNet.h \
-  /Applications/Eos.app/Eos/include/./NeuralNet.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcNeuralNet.h
 test.o: test.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
   ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleLearning.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h
+  /usr/include/sys/syslimits.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleLearning.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleLearning.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageNeuralNetParticleLearning.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageNeuralNetParticleLearning.h

diff --git a/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/Makefile b/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/Makefile
+++ b/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/mrcImageNeuralNetParticleLearning b/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/mrcImageNeuralNetParticleLearning
index 3e3b499..a366515 100755 (executable)
Binary files a/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/mrcImageNeuralNetParticleLearning and b/src/Tools/pickup/mrcImageNeuralNetParticleLearning/src/X86MAC64/mrcImageNeuralNetParticleLearning differ

diff --git a/src/Tools/psUtil/psFileMerge/src/X86MAC64/.Depend b/src/Tools/psUtil/psFileMerge/src/X86MAC64/.Depend
index 232e326..3297445 100644 (file)
--- a/src/Tools/psUtil/psFileMerge/src/X86MAC64/.Depend
+++ b/src/Tools/psUtil/psFileMerge/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/psFileMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/psFileMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/psFileMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/psFileMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,59 +91,115 @@ psFileMerge.o: psFileMerge.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/psFile.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/psFile.h \
   /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
-  ../inc/../inc/psFileMerge.h /Applications/Eos.app/Eos/include/genUtil.h
+  ../inc/../inc/psFileMerge.h \
+  /Applications/Eos.app/Eos/include/genUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/psFileMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/psFileMerge.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/psFileMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/psFileMerge.h

diff --git a/src/Tools/psUtil/psFileMerge/src/X86MAC64/Makefile b/src/Tools/psUtil/psFileMerge/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/psUtil/psFileMerge/src/X86MAC64/Makefile
+++ b/src/Tools/psUtil/psFileMerge/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/psUtil/psFileMerge/src/X86MAC64/psFileMerge b/src/Tools/psUtil/psFileMerge/src/X86MAC64/psFileMerge
index 33b0b9d..9782a3c 100755 (executable)
Binary files a/src/Tools/psUtil/psFileMerge/src/X86MAC64/psFileMerge and b/src/Tools/psUtil/psFileMerge/src/X86MAC64/psFileMerge differ

diff --git a/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/.Depend b/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/.Depend
index 0151688..1d199ab 100644 (file)
--- a/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/.Depend
+++ b/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/psFilePageMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/psFilePageMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/psFilePageMerge.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/psFilePageMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,26 +91,43 @@ psFilePageMerge.o: psFilePageMerge.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/psFile.h \
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/psFile.h \
   /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
   ../inc/../inc/psFilePageMerge.h \
   /Applications/Eos.app/Eos/include/genUtil.h
@@ -89,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/psFilePageMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/psFilePageMerge.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/psFilePageMerge.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/psFilePageMerge.h

diff --git a/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/Makefile b/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/Makefile
+++ b/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/psFilePageMerge b/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/psFilePageMerge
index ef13674..9037361 100755 (executable)
Binary files a/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/psFilePageMerge and b/src/Tools/psUtil/psFilePageMerge/src/X86MAC64/psFilePageMerge differ

diff --git a/src/Tools/random/randomNormalGet/src/X86MAC64/.Depend b/src/Tools/random/randomNormalGet/src/X86MAC64/.Depend
index 4ddc18f..2d89ba2 100644 (file)
--- a/src/Tools/random/randomNormalGet/src/X86MAC64/.Depend
+++ b/src/Tools/random/randomNormalGet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/randomNormalGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/randomNormalGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/randomNormalGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/randomNormalGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,21 +91,43 @@ randomNormalGet.o: randomNormalGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/randomNormalGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/randomNormalGet.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/mrcImage.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -86,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/randomNormalGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/randomNormalGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/randomNormalGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/randomNormalGet.h

diff --git a/src/Tools/random/randomNormalGet/src/X86MAC64/Makefile b/src/Tools/random/randomNormalGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/random/randomNormalGet/src/X86MAC64/Makefile
+++ b/src/Tools/random/randomNormalGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/random/randomNormalGet/src/X86MAC64/randomNormalGet b/src/Tools/random/randomNormalGet/src/X86MAC64/randomNormalGet
index 1b12e24..bc7452b 100755 (executable)
Binary files a/src/Tools/random/randomNormalGet/src/X86MAC64/randomNormalGet and b/src/Tools/random/randomNormalGet/src/X86MAC64/randomNormalGet differ

diff --git a/src/Tools/random/randomUniformGet/src/X86MAC64/.Depend b/src/Tools/random/randomUniformGet/src/X86MAC64/.Depend
index cfd4309..c0527b9 100644 (file)
--- a/src/Tools/random/randomUniformGet/src/X86MAC64/.Depend
+++ b/src/Tools/random/randomUniformGet/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/randomUniformGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/randomUniformGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/randomUniformGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/randomUniformGet.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,25 +91,44 @@ randomUniformGet.o: randomUniformGet.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/randomUniformGet.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/randomUniformGet.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /Applications/Eos.app/Eos/include/Memory.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -88,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/randomUniformGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/randomUniformGet.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/randomUniformGet.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/randomUniformGet.h

diff --git a/src/Tools/random/randomUniformGet/src/X86MAC64/Makefile b/src/Tools/random/randomUniformGet/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/random/randomUniformGet/src/X86MAC64/Makefile
+++ b/src/Tools/random/randomUniformGet/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/random/randomUniformGet/src/X86MAC64/randomUniformGet b/src/Tools/random/randomUniformGet/src/X86MAC64/randomUniformGet
index 7107498..5aecc38 100755 (executable)
Binary files a/src/Tools/random/randomUniformGet/src/X86MAC64/randomUniformGet and b/src/Tools/random/randomUniformGet/src/X86MAC64/randomUniformGet differ

diff --git a/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/.Depend b/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/.Depend
index 06de006..320cad2 100644 (file)
--- a/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/.Depend
@@ -3,62 +3,91 @@ CheckCommonLineData.o: CheckCommonLineData.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/CheckCommonLineData.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckCommonLineData.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/lCommonLineCalculation.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/CheckCommonLineData.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckCommonLineData.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -67,27 +96,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/CheckCommonLineData.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckCommonLineData.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -96,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CheckCommonLineData.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CheckCommonLineData.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CheckCommonLineData.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CheckCommonLineData.h

diff --git a/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/CheckCommonLineData b/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/CheckCommonLineData
index 9977372..3abbb7c 100755 (executable)
Binary files a/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/CheckCommonLineData and b/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/CheckCommonLineData differ

diff --git a/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/Makefile b/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/CheckCommonLineData/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/.Depend b/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/.Depend
index 2b9d1ae..25fa67b 100644 (file)
--- a/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/.Depend
@@ -3,58 +3,88 @@ CheckOfOrientation.o: CheckOfOrientation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/CheckOfOrientation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckOfOrientation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/String.h
+  /Applications/Eos.app/Eos/include/Array.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/CheckOfOrientation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckOfOrientation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,27 +93,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/CheckOfOrientation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckOfOrientation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -92,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CheckOfOrientation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CheckOfOrientation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CheckOfOrientation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CheckOfOrientation.h

diff --git a/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/CheckOfOrientation b/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/CheckOfOrientation
index 7065764..274c27c 100755 (executable)
Binary files a/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/CheckOfOrientation and b/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/CheckOfOrientation differ

diff --git a/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/Makefile b/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/CheckOfOrientation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/.Depend b/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/.Depend
index dbe11ae..d3d0d42 100644 (file)
--- a/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/.Depend
@@ -4,29 +4,44 @@ CheckOrientationByDegree.o: CheckOrientationByDegree.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/CheckOrientationByDegree.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckOrientationByDegree.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h
@@ -35,28 +50,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/CheckOrientationByDegree.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckOrientationByDegree.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -65,28 +94,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/CheckOrientationByDegree.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CheckOrientationByDegree.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -95,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CheckOrientationByDegree.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CheckOrientationByDegree.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CheckOrientationByDegree.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CheckOrientationByDegree.h

diff --git a/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/CheckOrientationByDegree b/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/CheckOrientationByDegree
index 1d71050..e965c6b 100755 (executable)
Binary files a/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/CheckOrientationByDegree and b/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/CheckOrientationByDegree differ

diff --git a/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/Makefile b/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/CheckOrientationByDegree/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/.Depend b/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/.Depend
index 2ebe6bd..61ee71c 100644 (file)
--- a/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/.Depend
@@ -3,62 +3,89 @@ CommonLineCalculation.o: CommonLineCalculation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/CommonLineCalculation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CommonLineCalculation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/lCommonLineCalculation.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h
+  /usr/include/sys/syslimits.h \
+  /Applications/Eos.app/Eos/include/lCommonLineCalculation.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/CommonLineCalculation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CommonLineCalculation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -67,28 +94,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/CommonLineCalculation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/CommonLineCalculation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -97,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CommonLineCalculation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CommonLineCalculation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/CommonLineCalculation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/CommonLineCalculation.h

diff --git a/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/CommonLineCalculation b/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/CommonLineCalculation
index 7c19107..442912d 100755 (executable)
Binary files a/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/CommonLineCalculation and b/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/CommonLineCalculation differ

diff --git a/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/Makefile b/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/CommonLineCalculation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/.Depend b/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/.Depend
index 5900c99..62709dd 100644 (file)
--- a/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/.Depend
@@ -1,27 +1,44 @@
-EvaluateCorrelationMapwithCommonLine.o:  \
- EvaluateCorrelationMapwithCommonLine.c /usr/include/stdio.h \
+EvaluateCorrelationMapwithCommonLine.o: \
+  EvaluateCorrelationMapwithCommonLine.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lEvaluateCorrelationMapwithCommonLine.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -31,28 +48,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,28 +92,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/EvaluateCorrelationMapwithCommonLine.h

diff --git a/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/EvaluateCorrelationMapwithCommonLine b/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/EvaluateCorrelationMapwithCommonLine
index 70b3159..9c8eddf 100755 (executable)
Binary files a/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/EvaluateCorrelationMapwithCommonLine and b/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/EvaluateCorrelationMapwithCommonLine differ

diff --git a/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/Makefile b/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/EvaluateCorrelationMapwithCommonLine/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/.Depend b/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/.Depend
index c0c72bf..e01b954 100644 (file)
--- a/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/.Depend
@@ -4,24 +4,41 @@ FETOrientationSearchByAnnealing.o: FETOrientationSearchByAnnealing.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByAnnealing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByAnnealing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lFETOrientationSearchByAnnealing.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -32,28 +49,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByAnnealing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByAnnealing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -62,28 +93,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByAnnealing.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByAnnealing.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -92,34 +137,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByAnnealing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByAnnealing.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByAnnealing.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByAnnealing.h

diff --git a/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/FETOrientationSearchByAnnealing b/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/FETOrientationSearchByAnnealing
index 3f0d9bf..34e6f5b 100755 (executable)
Binary files a/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/FETOrientationSearchByAnnealing and b/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/FETOrientationSearchByAnnealing differ

diff --git a/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/Makefile b/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/FETOrientationSearchByAnnealing/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/.Depend b/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/.Depend
index 72bb921..24f1c56 100644 (file)
--- a/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/.Depend
@@ -1,35 +1,48 @@
-FETOrientationSearchByFeatureAlignment.o:  \
- FETOrientationSearchByFeatureAlignment.c /usr/include/stdio.h \
+FETOrientationSearchByFeatureAlignment.o: \
+  FETOrientationSearchByFeatureAlignment.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByFeatureAlignment.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByFeatureAlignment.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lFETOrientationSearchByFeatureAlignment.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
@@ -42,28 +55,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByFeatureAlignment.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByFeatureAlignment.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -72,28 +99,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByFeatureAlignment.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByFeatureAlignment.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -102,34 +143,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByFeatureAlignment.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByFeatureAlignment.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/FETOrientationSearchByFeatureAlignment.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/FETOrientationSearchByFeatureAlignment.h

diff --git a/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/FETOrientationSearchByFeatureAlignment b/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/FETOrientationSearchByFeatureAlignment
index ec433a1..04c862d 100755 (executable)
Binary files a/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/FETOrientationSearchByFeatureAlignment and b/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/FETOrientationSearchByFeatureAlignment differ

diff --git a/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/Makefile b/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/FETOrientationSearchByFeatureAlignment/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/.Depend b/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/.Depend
index eed028b..63d9b44 100644 (file)
--- a/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/.Depend
@@ -1,27 +1,45 @@
-FETmapOrientationSearchBySimultaneousFitting.o:  \
- FETmapOrientationSearchBySimultaneousFitting.c /usr/include/stdio.h \
+FETmapOrientationSearchBySimultaneousFitting.o: \
+  FETmapOrientationSearchBySimultaneousFitting.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/FETmapOrientationSearchBySimultaneousFitting.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lFETmapOrientationSearchBySimultaneousFitting.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -31,28 +49,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/FETmapOrientationSearchBySimultaneousFitting.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,28 +94,43 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/FETmapOrientationSearchBySimultaneousFitting.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -91,34 +139,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/FETmapOrientationSearchBySimultaneousFitting.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/FETmapOrientationSearchBySimultaneousFitting.h

diff --git a/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/FETmapOrientationSearchBySimultaneousFitting b/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/FETmapOrientationSearchBySimultaneousFitting
index 9817738..53b7b2f 100755 (executable)
Binary files a/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/FETmapOrientationSearchBySimultaneousFitting and b/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/FETmapOrientationSearchBySimultaneousFitting differ

diff --git a/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/Makefile b/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/FETmapOrientationSearchBySimultaneousFitting/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/.Depend b/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/.Depend
index 4419475..545ccb5 100644 (file)
--- a/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/.Depend
@@ -1,27 +1,46 @@
-FETsmallMapSetCreate_forSimultaneousMinimization.o:  \
- FETsmallMapSetCreate_forSimultaneousMinimization.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+FETsmallMapSetCreate_forSimultaneousMinimization.o: \
+  FETsmallMapSetCreate_forSimultaneousMinimization.c \
+  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/FETsmallMapSetCreate_forSimultaneousMinimization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lFETsmallMapSetCreate_forSimultaneousMinimization.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -31,28 +50,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/FETsmallMapSetCreate_forSimultaneousMinimization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,28 +95,43 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/FETsmallMapSetCreate_forSimultaneousMinimization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -91,34 +140,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/FETsmallMapSetCreate_forSimultaneousMinimization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/FETsmallMapSetCreate_forSimultaneousMinimization.h

diff --git a/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/FETsmallMapSetCreate_forSimultaneousMinimization b/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/FETsmallMapSetCreate_forSimultaneousMinimization
index cd54b7e..e46acee 100755 (executable)
Binary files a/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/FETsmallMapSetCreate_forSimultaneousMinimization and b/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/FETsmallMapSetCreate_forSimultaneousMinimization differ

diff --git a/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/Makefile b/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/FETsmallMapSetCreate_forSimultaneousMinimization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/.Depend b/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/.Depend
index daa7cb1..158fd55 100644 (file)
--- a/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/.Depend
@@ -4,56 +4,85 @@ LCalculationForOrientationSearch.o: LCalculationForOrientationSearch.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/LCalculationForOrientationSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/LCalculationForOrientationSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h
+  /usr/include/sys/syslimits.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/LCalculationForOrientationSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/LCalculationForOrientationSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -62,28 +91,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/LCalculationForOrientationSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/LCalculationForOrientationSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -92,34 +135,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/LCalculationForOrientationSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/LCalculationForOrientationSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/LCalculationForOrientationSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/LCalculationForOrientationSearch.h

diff --git a/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/LCalculationForOrientationSearch b/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/LCalculationForOrientationSearch
index e9c4714..f8fa605 100755 (executable)
Binary files a/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/LCalculationForOrientationSearch and b/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/LCalculationForOrientationSearch differ

diff --git a/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/Makefile b/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/LCalculationForOrientationSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/.Depend b/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/.Depend
index 8303e2a..8ed4301 100644 (file)
--- a/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/.Depend
@@ -4,29 +4,44 @@ ProjectionDirectionMapCreate.o: ProjectionDirectionMapCreate.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ProjectionDirectionMapCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ProjectionDirectionMapCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h
@@ -35,28 +50,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ProjectionDirectionMapCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ProjectionDirectionMapCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -65,28 +94,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/ProjectionDirectionMapCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ProjectionDirectionMapCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -95,34 +138,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ProjectionDirectionMapCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ProjectionDirectionMapCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/ProjectionDirectionMapCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ProjectionDirectionMapCreate.h

diff --git a/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/Makefile b/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/ProjectionDirectionMapCreate b/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/ProjectionDirectionMapCreate
index fada0ec..0f21935 100755 (executable)
Binary files a/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/ProjectionDirectionMapCreate and b/src/Tools/rec3d/ProjectionDirectionMapCreate/src/X86MAC64/ProjectionDirectionMapCreate differ

diff --git a/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/.Depend b/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/.Depend
index 26773f2..cccca6a 100644 (file)
--- a/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/.Depend
@@ -1,72 +1,96 @@
-WeightCalculationOfCommonLineSearch.o:  \
- WeightCalculationOfCommonLineSearch.c /usr/include/stdio.h \
+WeightCalculationOfCommonLineSearch.o: \
+  WeightCalculationOfCommonLineSearch.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/WeightCalculationOfCommonLineSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/WeightCalculationOfCommonLineSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/lmrcImageSinogram.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrcImageFileListAndEulerAngleDataRead.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/lCommonLineCalculation.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/WeightCalculationOfCommonLineSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/WeightCalculationOfCommonLineSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -75,28 +99,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/WeightCalculationOfCommonLineSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/WeightCalculationOfCommonLineSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -105,34 +143,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/WeightCalculationOfCommonLineSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/WeightCalculationOfCommonLineSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/WeightCalculationOfCommonLineSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/WeightCalculationOfCommonLineSearch.h

diff --git a/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/Makefile b/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/WeightCalculationOfCommonLineSearch b/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/WeightCalculationOfCommonLineSearch
index f5fc9f9..0e40754 100755 (executable)
Binary files a/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/WeightCalculationOfCommonLineSearch and b/src/Tools/rec3d/WeightCalculationOfCommonLineSearch/src/X86MAC64/WeightCalculationOfCommonLineSearch differ

diff --git a/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/.Depend b/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/.Depend
index b0fd6a2..f62c895 100644 (file)
--- a/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/.Depend
@@ -1,66 +1,96 @@
-WeightCalculationOfCommonLineSearchByAllSinogram.o:  \
- WeightCalculationOfCommonLineSearchByAllSinogram.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+WeightCalculationOfCommonLineSearchByAllSinogram.o: \
+  WeightCalculationOfCommonLineSearchByAllSinogram.c \
+  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/WeightCalculationOfCommonLineSearchByAllSinogram.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/String.h
+  /Applications/Eos.app/Eos/include/Array.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/WeightCalculationOfCommonLineSearchByAllSinogram.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -69,28 +99,43 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/WeightCalculationOfCommonLineSearchByAllSinogram.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -99,34 +144,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/WeightCalculationOfCommonLineSearchByAllSinogram.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/WeightCalculationOfCommonLineSearchByAllSinogram.h

diff --git a/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/Makefile b/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/WeightCalculationOfCommonLineSearchByAllSinogram b/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/WeightCalculationOfCommonLineSearchByAllSinogram
index 9e6e6c5..1bd0971 100755 (executable)
Binary files a/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/WeightCalculationOfCommonLineSearchByAllSinogram and b/src/Tools/rec3d/WeightCalculationOfCommonLineSearchByAllSinogram/src/X86MAC64/WeightCalculationOfCommonLineSearchByAllSinogram differ

diff --git a/src/Tools/rec3d/calcCommonLine/src/X86MAC64/.Depend b/src/Tools/rec3d/calcCommonLine/src/X86MAC64/.Depend
index 96a0c7c..cc81cca 100644 (file)
--- a/src/Tools/rec3d/calcCommonLine/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/calcCommonLine/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/calcCommonLine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/calcCommonLine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/calcCommonLine.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/calcCommonLine.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/calcCommonLine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/calcCommonLine.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/calcCommonLine.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/calcCommonLine.h

diff --git a/src/Tools/rec3d/calcCommonLine/src/X86MAC64/Makefile b/src/Tools/rec3d/calcCommonLine/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/calcCommonLine/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/calcCommonLine/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/.Depend b/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/.Depend
index fc8c9ce..10cb53d 100644 (file)
--- a/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/commonLinesSearchByVoting.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/commonLinesSearchByVoting.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/commonLinesSearchByVoting.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/commonLinesSearchByVoting.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/commonLinesSearchByVoting.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/commonLinesSearchByVoting.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/commonLinesSearchByVoting.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/commonLinesSearchByVoting.h

diff --git a/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/Makefile b/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/commonLinesSearchByVoting/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/ll2ltlg/src/X86MAC64/.Depend b/src/Tools/rec3d/ll2ltlg/src/X86MAC64/.Depend
index 5d4ddd1..a212cbd 100644 (file)
--- a/src/Tools/rec3d/ll2ltlg/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/ll2ltlg/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ll2ltlg.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ll2ltlg.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ll2ltlg.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ll2ltlg.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,70 +91,117 @@ ll2ltlg.o: ll2ltlg.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ll2ltlg.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ll2ltlg.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h \
+  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/ltlgData.h \
-  /Applications/Eos.app/Eos/include/lll2ltlg.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/ltlgData.h
+  /Applications/Eos.app/Eos/include/lll2ltlg.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ll2ltlg.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ll2ltlg.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ll2ltlg.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ll2ltlg.h

diff --git a/src/Tools/rec3d/ll2ltlg/src/X86MAC64/Makefile b/src/Tools/rec3d/ll2ltlg/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/ll2ltlg/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/ll2ltlg/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/ll2ltlg/src/X86MAC64/ll2ltlg b/src/Tools/rec3d/ll2ltlg/src/X86MAC64/ll2ltlg
index 547445e..d8a2f62 100755 (executable)
Binary files a/src/Tools/rec3d/ll2ltlg/src/X86MAC64/ll2ltlg and b/src/Tools/rec3d/ll2ltlg/src/X86MAC64/ll2ltlg differ

diff --git a/src/Tools/rec3d/llExtract/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtract/src/X86MAC64/.Depend
index e165e35..e0ecbd6 100644 (file)
--- a/src/Tools/rec3d/llExtract/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtract/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,73 +91,123 @@ llExtract.o: llExtract.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/llExtract.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtract.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllExtract.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllDataFit.h \
   /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtract.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/llExtract.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtract.h

diff --git a/src/Tools/rec3d/llExtract/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtract/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtract/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtract/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtract/src/X86MAC64/llExtract b/src/Tools/rec3d/llExtract/src/X86MAC64/llExtract
index ba043d0..87ba701 100755 (executable)
Binary files a/src/Tools/rec3d/llExtract/src/X86MAC64/llExtract and b/src/Tools/rec3d/llExtract/src/X86MAC64/llExtract differ

diff --git a/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/.Depend
index d1f78f3..793c2fb 100644 (file)
--- a/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractCtfinfFileCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractCtfinfFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractCtfinfFileCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractCtfinfFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,23 +92,40 @@ llExtractCtfinfFileCreate.o: llExtractCtfinfFileCreate.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractCtfinfFileCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractCtfinfFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lllExtractCtfinfFileCreate.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/ctfZeroPoint.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -88,34 +133,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractCtfinfFileCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractCtfinfFileCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractCtfinfFileCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractCtfinfFileCreate.h

diff --git a/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/llExtractCtfinfFileCreate b/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/llExtractCtfinfFileCreate
index d6bde20..86826fb 100755 (executable)
Binary files a/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/llExtractCtfinfFileCreate and b/src/Tools/rec3d/llExtractCtfinfFileCreate/src/X86MAC64/llExtractCtfinfFileCreate differ

diff --git a/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/.Depend
index 9d73a42..c9f4cd3 100644 (file)
--- a/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractCtrlFileCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractCtrlFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractCtrlFileCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractCtrlFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,31 +91,45 @@ llExtractCtrlFileCreate.o: llExtractCtrlFileCreate.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractCtrlFileCreate.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractCtrlFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -99,34 +141,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractCtrlFileCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractCtrlFileCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractCtrlFileCreate.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractCtrlFileCreate.h

diff --git a/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/llExtractCtrlFileCreate b/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/llExtractCtrlFileCreate
index 463469f..c91e8be 100755 (executable)
Binary files a/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/llExtractCtrlFileCreate and b/src/Tools/rec3d/llExtractCtrlFileCreate/src/X86MAC64/llExtractCtrlFileCreate differ

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/.Depend
index 0cd99cc..3dd64af 100644 (file)
--- a/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,42 +92,52 @@ llExtractWithLayerSeparation.o: llExtractWithLayerSeparation.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/llData.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/lllExtract.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/lllDataFit.h \
   /Applications/Eos.app/Eos/include/lllDatarMaxLimit.h \
   /Applications/Eos.app/Eos/include/lllDataLowPassFiltering.h \
@@ -107,46 +145,80 @@ llExtractWithLayerSeparation.o: llExtractWithLayerSeparation.c \
   /Applications/Eos.app/Eos/include/lllDataMergeDifferentN.h \
   /Applications/Eos.app/Eos/include/lllDataContributionCalcDifferentN.h \
   /Applications/Eos.app/Eos/include/lllDataCTF.h \
-  /Applications/Eos.app/Eos/include/lllDataFit.h \
   /Applications/Eos.app/Eos/include/lllDataFitAndAverage.h \
   /Applications/Eos.app/Eos/include/lllDataFitParamInverse.h \
   /Applications/Eos.app/Eos/include/lllDataAxisSearch.h \
   /Applications/Eos.app/Eos/include/lllDataRescaling.h \
-  /Applications/Eos.app/Eos/include/lllDataCTFCompensation.h \
-  /Applications/Eos.app/Eos/include/lllDataFitAndAverage.h
+  /Applications/Eos.app/Eos/include/lllDataCTFCompensation.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparation.h

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/llExtractWithLayerSeparation b/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/llExtractWithLayerSeparation
index f071f0b..412261d 100755 (executable)
Binary files a/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/llExtractWithLayerSeparation and b/src/Tools/rec3d/llExtractWithLayerSeparation/src/X86MAC64/llExtractWithLayerSeparation differ

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/.Depend
index 5728053..95ccd76 100644 (file)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,56 +48,89 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-llExtractWithLayerSeparationCtrlFileCreate.o:  \
- llExtractWithLayerSeparationCtrlFileCreate.c /usr/include/stdio.h \
+llExtractWithLayerSeparationCtrlFileCreate.o: \
+  llExtractWithLayerSeparationCtrlFileCreate.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreate.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/llData.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h
@@ -91,34 +139,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreate.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreate.h

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreate b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreate
index 91e7a4e..0c8b618 100755 (executable)
Binary files a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreate and b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreate/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreate differ

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/.Depend
index 8720ddf..69eac94 100644 (file)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreateMyosin.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,50 +48,85 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreateMyosin.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-llExtractWithLayerSeparationCtrlFileCreateMyosin.o:  \
- llExtractWithLayerSeparationCtrlFileCreateMyosin.c /usr/include/stdio.h \
-  /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
+llExtractWithLayerSeparationCtrlFileCreateMyosin.o: \
+  llExtractWithLayerSeparationCtrlFileCreateMyosin.c \
+  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreateMyosin.h \
   /Applications/Eos.app/Eos/include/genUtil.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -84,34 +134,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreateMyosin.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationCtrlFileCreateMyosin.h

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreateMyosin b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreateMyosin
index f4501ef..43436c4 100755 (executable)
Binary files a/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreateMyosin and b/src/Tools/rec3d/llExtractWithLayerSeparationCtrlFileCreateMyosin/src/X86MAC64/llExtractWithLayerSeparationCtrlFileCreateMyosin differ

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/.Depend
index 640fb93..5ef1e50 100644 (file)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationFilamentInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +48,87 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationFilamentInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-llExtractWithLayerSeparationFilamentInfo.o:  \
- llExtractWithLayerSeparationFilamentInfo.c /usr/include/stdio.h \
+llExtractWithLayerSeparationFilamentInfo.o: \
+  llExtractWithLayerSeparationFilamentInfo.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationFilamentInfo.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +139,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationFilamentInfo.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/llExtractWithLayerSeparationFilamentInfo.h

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/llExtractWithLayerSeparationFilamentInfo b/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/llExtractWithLayerSeparationFilamentInfo
index 46dbc1c..70ea98c 100755 (executable)
Binary files a/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/llExtractWithLayerSeparationFilamentInfo and b/src/Tools/rec3d/llExtractWithLayerSeparationFilamentInfo/src/X86MAC64/llExtractWithLayerSeparationFilamentInfo differ

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/.Depend
index 64326db..a1fe25e 100644 (file)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationServer.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationServer.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationServer.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationServer.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationServer.h

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationServer/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/.Depend b/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/.Depend
index 16a80e1..05487be 100644 (file)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationSingle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationSingle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,54 +47,85 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationSingle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationSingle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-llExtractWithLayerSeparationSingle.o:  \
- llExtractWithLayerSeparationSingle.c /usr/include/stdio.h \
+llExtractWithLayerSeparationSingle.o: \
+  llExtractWithLayerSeparationSingle.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationSingle.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationSingle.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationSingle.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationSingle.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/llExtractWithLayerSeparationSingle.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/llExtractWithLayerSeparationSingle.h

diff --git a/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/Makefile b/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/llExtractWithLayerSeparationSingle/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/.Depend b/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/.Depend
index 8091cbe..a2519d7 100644 (file)
--- a/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlg2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlg2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlg2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlg2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,32 +91,46 @@ ltlg2mrc.o: ltlg2mrc.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlg2mrc.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlg2mrc.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/File.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/ltlgData.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -96,32 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ltlg2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ltlg2mrc.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ltlg2mrc.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ltlg2mrc.h

diff --git a/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/Makefile b/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/ltlg2mrc b/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/ltlg2mrc
index 11360a9..268984a 100755 (executable)
Binary files a/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/ltlg2mrc and b/src/Tools/rec3d/ltlg2mrc/src/X86MAC64/ltlg2mrc differ

diff --git a/src/Tools/rec3d/ltlg2ps/src/X86MAC64/.Depend b/src/Tools/rec3d/ltlg2ps/src/X86MAC64/.Depend
index c84740e..a470d53 100644 (file)
--- a/src/Tools/rec3d/ltlg2ps/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/ltlg2ps/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlg2ps.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlg2ps.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/ltlg2ps.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/ltlg2ps.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,32 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ltlg2ps.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ltlg2ps.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/ltlg2ps.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/ltlg2ps.h

diff --git a/src/Tools/rec3d/ltlg2ps/src/X86MAC64/Makefile b/src/Tools/rec3d/ltlg2ps/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/ltlg2ps/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/ltlg2ps/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/.Depend b/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/.Depend
index 672074b..ce218cb 100644 (file)
--- a/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2Dto3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2Dto3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,44 +91,67 @@ mrc2Dto3D.o: mrc2Dto3D.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc2Dto3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/eosPThread.h /usr/include/pthread.h \
   /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h \
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_mach_port_t.h /usr/include/errno.h \
+  /usr/include/sys/errno.h /usr/include/sys/_types/_errno_t.h \
   /Applications/Eos.app/Eos/include/lmrcImageRhoFiltering.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrc2Dto3D.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /Applications/Eos.app/Eos/include/String.h \
-  /Applications/Eos.app/Eos/include/lmrcImageRhoFiltering.h \
   /Applications/Eos.app/Eos/include/lmrcImageMultiplying.h \
   /Applications/Eos.app/Eos/include/lmrc3Dto2D.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -106,32 +159,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2Dto3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc2Dto3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3D.h

diff --git a/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/Makefile b/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/mrc2Dto3D b/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/mrc2Dto3D
index 2e3862d..f39e7e2 100755 (executable)
Binary files a/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/mrc2Dto3D and b/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/mrc2Dto3D differ

diff --git a/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/.Depend b/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/.Depend
index 39d6285..3bb0c5f 100644 (file)
--- a/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrc2Dto3DforVariation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3DforVariation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrc2Dto3DforVariation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3DforVariation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrc2Dto3DforVariation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3DforVariation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrc2Dto3DforVariation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc2Dto3DforVariation.h

diff --git a/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/Makefile b/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrc2Dto3DforVariation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/.Depend b/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/.Depend
index 7663bf7..7f7825f 100644 (file)
--- a/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc3Dto2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc3Dto2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc3Dto2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc3Dto2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,65 +91,130 @@ mrc3Dto2D.o: mrc3Dto2D.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrc3Dto2D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrc3Dto2D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/lmrc3Dto2D.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
   /Applications/Eos.app/Eos/include/lmrc3Dto2D.h \
   /Applications/Eos.app/Eos/include/eosPThread.h /usr/include/pthread.h \
   /usr/include/pthread_impl.h /usr/include/sched.h /usr/include/time.h \
-  /usr/include/_structs.h /usr/include/errno.h /usr/include/sys/errno.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h \
+  /usr/include/sys/_types/_pthread_cond_t.h \
+  /usr/include/sys/_types/_pthread_condattr_t.h \
+  /usr/include/sys/_types/_pthread_key_t.h \
+  /usr/include/sys/_types/_pthread_mutex_t.h \
+  /usr/include/sys/_types/_pthread_mutexattr_t.h \
+  /usr/include/sys/_types/_pthread_once_t.h \
+  /usr/include/sys/_types/_pthread_rwlock_t.h \
+  /usr/include/sys/_types/_pthread_rwlockattr_t.h \
+  /usr/include/sys/_types/_pthread_t.h \
+  /usr/include/sys/_types/_mach_port_t.h /usr/include/errno.h \
+  /usr/include/sys/errno.h /usr/include/sys/_types/_errno_t.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc3Dto2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc3Dto2D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h ../inc/../inc/mrc3Dto2D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrc3Dto2D.h

diff --git a/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/Makefile b/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/mrc3Dto2D b/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/mrc3Dto2D
index 7b59dc0..f0b757f 100755 (executable)
Binary files a/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/mrc3Dto2D and b/src/Tools/rec3d/mrc3Dto2D/src/X86MAC64/mrc3Dto2D differ

diff --git a/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/.Depend
index 09a3e4f..00f09de 100644 (file)
--- a/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCommonLineSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCommonLineSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCommonLineSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCommonLineSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,24 +92,41 @@ mrcImageCommonLineSearch.o: mrcImageCommonLineSearch.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageCommonLineSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageCommonLineSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lmrcImageCommonLine.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -91,34 +136,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCommonLineSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCommonLineSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageCommonLineSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageCommonLineSearch.h

diff --git a/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/mrcImageCommonLineSearch b/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/mrcImageCommonLineSearch
index 1747d91..da98733 100755 (executable)
Binary files a/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/mrcImageCommonLineSearch and b/src/Tools/rec3d/mrcImageCommonLineSearch/src/X86MAC64/mrcImageCommonLineSearch differ

diff --git a/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/.Depend
index c619f07..be0172d 100644 (file)
--- a/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageInverseRadonTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageInverseRadonTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageInverseRadonTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageInverseRadonTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,31 +92,45 @@ mrcImageInverseRadonTransform.o: mrcImageInverseRadonTransform.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageInverseRadonTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageInverseRadonTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -98,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageInverseRadonTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageInverseRadonTransform.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageInverseRadonTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageInverseRadonTransform.h

diff --git a/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/mrcImageInverseRadonTransform b/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/mrcImageInverseRadonTransform
index 302bde7..e7b27f6 100755 (executable)
Binary files a/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/mrcImageInverseRadonTransform and b/src/Tools/rec3d/mrcImageInverseRadonTransform/src/X86MAC64/mrcImageInverseRadonTransform differ

diff --git a/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/.Depend
index 76478b8..25db537 100644 (file)
--- a/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageOrientationSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOrientationSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageOrientationSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOrientationSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -64,69 +92,119 @@ mrcImageOrientationSearch.o: mrcImageOrientationSearch.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageOrientationSearch.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageOrientationSearch.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/lCommonLineCalculation.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOrientationSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOrientationSearch.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageOrientationSearch.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageOrientationSearch.h

diff --git a/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/mrcImageOrientationSearch b/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/mrcImageOrientationSearch
index 5c3ab5d..0f11b06 100755 (executable)
Binary files a/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/mrcImageOrientationSearch and b/src/Tools/rec3d/mrcImageOrientationSearch/src/X86MAC64/mrcImageOrientationSearch differ

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/.Depend
index 58ba23b..e69f516 100644 (file)
--- a/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHigherSelection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,93 +48,162 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHigherSelection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageOrientationSearchByHigherSelection.o:  \
- mrcImageOrientationSearchByHigherSelection.c /usr/include/stdio.h \
+mrcImageOrientationSearchByHigherSelection.o: \
+  mrcImageOrientationSearchByHigherSelection.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHigherSelection.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h
+  /usr/include/sys/syslimits.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHigherSelection.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHigherSelection.h

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/mrcImageOrientationSearchByHigherSelection b/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/mrcImageOrientationSearchByHigherSelection
index f74689d..69e0cb2 100755 (executable)
Binary files a/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/mrcImageOrientationSearchByHigherSelection and b/src/Tools/rec3d/mrcImageOrientationSearchByHigherSelection/src/X86MAC64/mrcImageOrientationSearchByHigherSelection differ

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/.Depend
index d9bdad5..777e7cb 100644 (file)
--- a/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHybridization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,61 +48,94 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHybridization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
-mrcImageOrientationSearchByHybridization.o:  \
- mrcImageOrientationSearchByHybridization.c /usr/include/stdio.h \
+mrcImageOrientationSearchByHybridization.o: \
+  mrcImageOrientationSearchByHybridization.c /usr/include/stdio.h \
   /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /usr/include/time.h /usr/include/_structs.h \
+  /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \
+  /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \
   ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHybridization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h
@@ -96,34 +144,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHybridization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchByHybridization.h

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/mrcImageOrientationSearchByHybridization b/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/mrcImageOrientationSearchByHybridization
index f90a4e2..47cefb4 100755 (executable)
Binary files a/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/mrcImageOrientationSearchByHybridization and b/src/Tools/rec3d/mrcImageOrientationSearchByHybridization/src/X86MAC64/mrcImageOrientationSearchByHybridization differ

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/.Depend
index 7bb64c8..340302c 100644 (file)
--- a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/.Depend
@@ -3,28 +3,43 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchBySimultaneousMinimization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +48,43 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchBySimultaneousMinimization.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +93,72 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchBySimultaneousMinimization.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h \
   ../inc/../inc/mrcImageOrientationSearchBySimultaneousMinimization.h

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/.Depend
index dd40758..7c59904 100644 (file)
--- a/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadonTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadonTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadonTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadonTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,23 +91,40 @@ mrcImageRadonTransform.o: mrcImageRadonTransform.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadonTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadonTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -89,34 +134,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadonTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadonTransform.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcImageRadonTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcImageRadonTransform.h

diff --git a/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/mrcImageRadonTransform b/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/mrcImageRadonTransform
index d2e094e..b30da7a 100755 (executable)
Binary files a/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/mrcImageRadonTransform and b/src/Tools/rec3d/mrcImageRadonTransform/src/X86MAC64/mrcImageRadonTransform differ

diff --git a/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/.Depend b/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/.Depend
index 92824b8..abb3d11 100644 (file)
--- a/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/.Depend
+++ b/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,70 +91,119 @@ mrcRadon2Dto3D.o: mrcRadon2Dto3D.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/String.h \
+  /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
   /Applications/Eos.app/Eos/include/Array.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/lmrcImageRhoFiltering.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h
+  /Applications/Eos.app/Eos/include/lmrcImageRhoFiltering.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRadon2Dto3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/mrcRadon2Dto3D.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/mrcRadon2Dto3D.h

diff --git a/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/Makefile b/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/Makefile
+++ b/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/mrcRadon2Dto3D b/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/mrcRadon2Dto3D
index 0fba0d9..32d6f10 100755 (executable)
Binary files a/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/mrcRadon2Dto3D and b/src/Tools/rec3d/mrcRadon2Dto3D/src/X86MAC64/mrcRadon2Dto3D differ

diff --git a/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/.Depend b/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/.Depend
index a66c95b..f94b1d5 100644 (file)
--- a/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/.Depend
+++ b/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,34 +91,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelCheck.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelCheck.h

diff --git a/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/Makefile b/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/Makefile
+++ b/src/Tools/simulation/energyTransferModelCheck/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/.Depend b/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/.Depend
index a313211..5003733 100644 (file)
--- a/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/.Depend
+++ b/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelResultCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelResultCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -34,31 +48,45 @@ energyTransferModelResultCheck.o: energyTransferModelResultCheck.c \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelResultCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelResultCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h /Applications/Eos.app/Eos/include/lFRET.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
@@ -68,28 +96,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelResultCheck.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelResultCheck.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -98,34 +140,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelResultCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelResultCheck.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/energyTransferModelResultCheck.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/energyTransferModelResultCheck.h

diff --git a/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/Makefile b/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/Makefile
+++ b/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/energyTransferModelResultCheck b/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/energyTransferModelResultCheck
index 2844342..07e07ed 100755 (executable)
Binary files a/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/energyTransferModelResultCheck and b/src/Tools/simulation/energyTransferModelResultCheck/src/X86MAC64/energyTransferModelResultCheck differ

diff --git a/src/Tools/simulation/muscleSimulation/src/X86MAC64/.Depend b/src/Tools/simulation/muscleSimulation/src/X86MAC64/.Depend
index c308a40..091f7b1 100644 (file)
--- a/src/Tools/simulation/muscleSimulation/src/X86MAC64/.Depend
+++ b/src/Tools/simulation/muscleSimulation/src/X86MAC64/.Depend
@@ -3,27 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/muscleSimulation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/muscleSimulation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -32,27 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/muscleSimulation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/muscleSimulation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -61,55 +91,112 @@ muscleSimulation.o: muscleSimulation.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/muscleSimulation.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/muscleSimulation.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Random.h /usr/include/time.h \
-  /usr/include/_structs.h
+  /usr/include/_structs.h /usr/include/sys/_structs.h \
+  /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_clock_t.h \
+  /usr/include/sys/_types/_time_t.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/muscleSimulation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/muscleSimulation.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/muscleSimulation.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/muscleSimulation.h

diff --git a/src/Tools/simulation/muscleSimulation/src/X86MAC64/Makefile b/src/Tools/simulation/muscleSimulation/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/simulation/muscleSimulation/src/X86MAC64/Makefile
+++ b/src/Tools/simulation/muscleSimulation/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/transform/Descartes2Polar/src/X86MAC64/.Depend b/src/Tools/transform/Descartes2Polar/src/X86MAC64/.Depend
index 3916567..d29548a 100644 (file)
--- a/src/Tools/transform/Descartes2Polar/src/X86MAC64/.Depend
+++ b/src/Tools/transform/Descartes2Polar/src/X86MAC64/.Depend
@@ -3,19 +3,38 @@ Descartes2Polar.o: Descartes2Polar.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Descartes2Polar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Descartes2Polar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -23,27 +42,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Descartes2Polar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Descartes2Polar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Descartes2Polar.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Descartes2Polar.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/Descartes2Polar.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/Descartes2Polar.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/Descartes2Polar.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/Descartes2Polar.h

diff --git a/src/Tools/transform/Descartes2Polar/src/X86MAC64/Descartes2Polar b/src/Tools/transform/Descartes2Polar/src/X86MAC64/Descartes2Polar
index 49d8ce2..afff214 100755 (executable)
Binary files a/src/Tools/transform/Descartes2Polar/src/X86MAC64/Descartes2Polar and b/src/Tools/transform/Descartes2Polar/src/X86MAC64/Descartes2Polar differ

diff --git a/src/Tools/transform/Descartes2Polar/src/X86MAC64/Makefile b/src/Tools/transform/Descartes2Polar/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/transform/Descartes2Polar/src/X86MAC64/Makefile
+++ b/src/Tools/transform/Descartes2Polar/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/transform/Polar2Descartes/src/X86MAC64/.Depend b/src/Tools/transform/Polar2Descartes/src/X86MAC64/.Depend
index 04b9c20..e5ad464 100644 (file)
--- a/src/Tools/transform/Polar2Descartes/src/X86MAC64/.Depend
+++ b/src/Tools/transform/Polar2Descartes/src/X86MAC64/.Depend
@@ -3,19 +3,38 @@ Polar2Descartes.o: Polar2Descartes.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Polar2Descartes.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Polar2Descartes.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/lDescartesIntoPolar.h
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
@@ -23,27 +42,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Polar2Descartes.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Polar2Descartes.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -52,27 +86,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h ../inc/../inc/Polar2Descartes.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/Polar2Descartes.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -81,34 +130,70 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/Polar2Descartes.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/Polar2Descartes.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/Polar2Descartes.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/Polar2Descartes.h

diff --git a/src/Tools/transform/Polar2Descartes/src/X86MAC64/Makefile b/src/Tools/transform/Polar2Descartes/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/transform/Polar2Descartes/src/X86MAC64/Makefile
+++ b/src/Tools/transform/Polar2Descartes/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/transform/Polar2Descartes/src/X86MAC64/Polar2Descartes b/src/Tools/transform/Polar2Descartes/src/X86MAC64/Polar2Descartes
index cce37dc..5ed2f1e 100755 (executable)
Binary files a/src/Tools/transform/Polar2Descartes/src/X86MAC64/Polar2Descartes and b/src/Tools/transform/Polar2Descartes/src/X86MAC64/Polar2Descartes differ

diff --git a/src/Tools/transform/pointAffineTransform/src/X86MAC64/.Depend b/src/Tools/transform/pointAffineTransform/src/X86MAC64/.Depend
index eb9243f..aacab07 100644 (file)
--- a/src/Tools/transform/pointAffineTransform/src/X86MAC64/.Depend
+++ b/src/Tools/transform/pointAffineTransform/src/X86MAC64/.Depend
@@ -3,28 +3,42 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pointAffineTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pointAffineTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -33,28 +47,42 @@ init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pointAffineTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pointAffineTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/String.h \
   /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h
@@ -63,58 +91,111 @@ pointAffineTransform.o: pointAffineTransform.c /usr/include/stdio.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h ../inc/config.h \
-  ../inc/../inc/pointAffineTransform.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  ../inc/config.h ../inc/../inc/pointAffineTransform.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Array.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pointAffineTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pointAffineTransform.h
 util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/secure/_stdio.h \
-  /usr/include/secure/_common.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h ../inc/config.h \
-  ../inc/../inc/pointAffineTransform.h
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/pointAffineTransform.h

diff --git a/src/Tools/transform/pointAffineTransform/src/X86MAC64/Makefile b/src/Tools/transform/pointAffineTransform/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/transform/pointAffineTransform/src/X86MAC64/Makefile
+++ b/src/Tools/transform/pointAffineTransform/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/transform/pointAffineTransform/src/X86MAC64/pointAffineTransform b/src/Tools/transform/pointAffineTransform/src/X86MAC64/pointAffineTransform
index 804d3c6..36a1962 100755 (executable)
Binary files a/src/Tools/transform/pointAffineTransform/src/X86MAC64/pointAffineTransform and b/src/Tools/transform/pointAffineTransform/src/X86MAC64/pointAffineTransform differ

diff --git a/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/.Depend b/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/.Depend
index e4eaf1d..d12f4fc 100644 (file)
--- a/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/.Depend
+++ b/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/.Depend
@@ -1,210 +1,259 @@
-vectorImageNearestNeighborMethod.o: vectorImageNearestNeighborMethod.cc \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/File.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
   ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/vectorImageNearestNeighborMethod.h
-vectorImageNearestNeighborMethod.o: vectorImageNearestNeighborMethod.cc \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/syslimits.h
+init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/File.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
   ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
+  /Applications/Eos.app/Eos/include/File.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/vectorImageNearestNeighborMethod.h
-vectorImageNearestNeighborMethod.o: vectorImageNearestNeighborMethod.cc \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/syslimits.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/File.h \
-  ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/vectorImageNearestNeighborMethod.h
-vectorImageNearestNeighborMethod.o: vectorImageNearestNeighborMethod.cc \
-  /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h
+util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/File.h \
-  ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /usr/include/limits.h /usr/include/machine/limits.h \
-  /usr/include/i386/limits.h /usr/include/i386/_limits.h \
-  /usr/include/sys/syslimits.h \
-  /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
-  /Applications/Eos.app/Eos/include/ctfInfo.h \
-  /Applications/Eos.app/Eos/include/Vector.h \
-  /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/vectorImageNearestNeighborMethod.h
-vectorImageNearestNeighborMethod.o: vectorImageNearestNeighborMethod.cc \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h
+vectorImageNearestNeighborMethod.o: vectorImageNearestNeighborMethod.c \
   /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/File.h \
-  ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
+  ../inc/../inc/vectorImageNearestNeighborMethod.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/vectorImageNearestNeighborMethod.h
+  /Applications/Eos.app/Eos/include/Array.h
 vectorImageNearestNeighborMethod.o: vectorImageNearestNeighborMethod.cc \
   /usr/include/stdio.h /usr/include/sys/cdefs.h \
   /usr/include/sys/_symbol_aliasing.h \
   /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
   /usr/include/AvailabilityInternal.h /usr/include/_types.h \
   /usr/include/sys/_types.h /usr/include/machine/_types.h \
-  /usr/include/i386/_types.h /usr/include/stdlib.h \
-  /usr/include/sys/wait.h /usr/include/sys/signal.h \
-  /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
-  /usr/include/i386/signal.h /usr/include/i386/_structs.h \
-  /usr/include/sys/_structs.h /usr/include/machine/_structs.h \
-  /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+  /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
+  /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
+  /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
+  /usr/include/stdlib.h /usr/include/sys/wait.h \
+  /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
+  /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
+  /usr/include/machine/signal.h /usr/include/i386/signal.h \
+  /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
+  /usr/include/mach/i386/_structs.h \
+  /usr/include/sys/_types/_sigaltstack.h \
+  /usr/include/sys/_types/_ucontext.h \
+  /usr/include/sys/_types/_pthread_attr_t.h \
+  /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
+  /usr/include/sys/resource.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/stdint.h \
+  /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
+  /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
+  /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
+  /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
+  /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
+  /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
+  /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
   /usr/include/machine/endian.h /usr/include/i386/endian.h \
   /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
   /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
-  /usr/include/machine/types.h /usr/include/i386/types.h \
-  /usr/include/i386/_types.h /Applications/Eos.app/Eos/include/string.h \
-  /usr/include/math.h /Applications/Eos.app/Eos/include/File.h \
-  ../inc/config.h ../inc/../inc/vectorImageNearestNeighborMethod.h \
+  /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
+  /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
+  /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
+  /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
+  /Applications/Eos.app/Eos/include/string.h /usr/include/math.h \
+  /Applications/Eos.app/Eos/include/File.h ../inc/config.h \
+  ../inc/../inc/vectorImageNearestNeighborMethod.h \
   /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/Memory.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h \
-  /Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/syslimits.h \
+  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.0/include/limits.h \
   /usr/include/limits.h /usr/include/machine/limits.h \
   /usr/include/i386/limits.h /usr/include/i386/_limits.h \
   /usr/include/sys/syslimits.h \
   /Applications/Eos.app/Eos/include/mrcImage.h \
-  /Applications/Eos.app/Eos/include/genUtil.h \
   /Applications/Eos.app/Eos/include/ctfInfo.h \
   /Applications/Eos.app/Eos/include/Vector.h \
   /Applications/Eos.app/Eos/include/Matrix3D.h \
-  /Applications/Eos.app/Eos/include/Array.h \
-  ../inc/vectorImageNearestNeighborMethod.h
+  /Applications/Eos.app/Eos/include/Array.h

diff --git a/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/Makefile b/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/Makefile
index 2a9beb5..ec61247 100755 (executable)
--- a/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/Makefile
+++ b/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/Makefile
@@ -78,8 +78,8 @@ $(OBJECTNAME): $(MODULES) $(LIBFILES)
        fi
        @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
        then \
-               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
-               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
        fi
 
 

diff --git a/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/vectorImageNearestNeighborMethod b/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/vectorImageNearestNeighborMethod
index a496b32..31017ca 100755 (executable)
Binary files a/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/vectorImageNearestNeighborMethod and b/src/Tools/vectorImage/vectorImageNearestNeighborMethod/src/X86MAC64/vectorImageNearestNeighborMethod differ

diff --git a/util/X86MAC64/include/GL b/util/X86MAC64/include/GL
new file mode 120000 (symlink)
index 0000000..b3718d6
--- /dev/null
+++ b/util/X86MAC64/include/GL
@@ -0,0 +1 @@
+/System/Library/Frameworks/OpenGL.framework/Headers
\ No newline at end of file

diff --git a/util/X86MAC64/lib/libgif.dylib b/util/X86MAC64/lib/libgif.dylib
index 529af0d..ff36f56 100755 (executable)
Binary files a/util/X86MAC64/lib/libgif.dylib and b/util/X86MAC64/lib/libgif.dylib differ

diff --git a/util/X86MAC64/lib/libtiff.dylib b/util/X86MAC64/lib/libtiff.dylib
index f62b867..e7e271c 100755 (executable)
Binary files a/util/X86MAC64/lib/libtiff.dylib and b/util/X86MAC64/lib/libtiff.dylib differ